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Conserved domains on  [gi|478440705|gb|ENN96862|]
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transcriptional regulator [Pseudoalteromonas agarivorans S816]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

Gene Ontology:  GO:0003677|GO:0003700
PubMed:  19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 2-294 3.51e-58

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 188.51  E-value: 3.51e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   2 KLPPLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNA 81
Cdd:PRK11139   4 RLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  82 SQMIRHGKS-GNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVgDQP-DYNDQFADCFI---TTNPPerNFVNQFM 156
Cdd:PRK11139  84 TRKLRARSAkGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAV-DRLeDFLRDDVDVAIrygRGNWP--GLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVCGKKLWQQlrNKPL--PDSLWQHPLLsvqYSDTNeslgDDWLRWCMSGKFElpkDVKINQ---FSHVLLAAE 231
Cdd:PRK11139 161 LDEYLLPVCSPALLNG--GKPLktPEDLARHTLL---HDDSR----EDWRAWFRAAGLD---DLNVQQgpiFSHSSMALQ 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478440705 232 AARYNLGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWLKQQ 294
Cdd:PRK11139 229 AAIHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAE 291
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 2-294 3.51e-58

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 188.51  E-value: 3.51e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   2 KLPPLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNA 81
Cdd:PRK11139   4 RLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  82 SQMIRHGKS-GNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVgDQP-DYNDQFADCFI---TTNPPerNFVNQFM 156
Cdd:PRK11139  84 TRKLRARSAkGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAV-DRLeDFLRDDVDVAIrygRGNWP--GLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVCGKKLWQQlrNKPL--PDSLWQHPLLsvqYSDTNeslgDDWLRWCMSGKFElpkDVKINQ---FSHVLLAAE 231
Cdd:PRK11139 161 LDEYLLPVCSPALLNG--GKPLktPEDLARHTLL---HDDSR----EDWRAWFRAAGLD---DLNVQQgpiFSHSSMALQ 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478440705 232 AARYNLGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWLKQQ 294
Cdd:PRK11139 229 AAIHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAE 291
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-295 1.49e-51

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.05  E-value: 1.49e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   5 PLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQM 84
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  85 IR---HGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNmVGDQPDYNDQFAD-----CFITTNPPERNFVNQFM 156
Cdd:COG0583   82 LRalrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELR-EGNSDRLVDALLEgeldlAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVCGKklwqqlrnkplpdslwQHPLLSvqysdtneslgddwlrwcmsgkfelpkdvKINQFSHVLLAAEAARYN 236
Cdd:COG0583  161 GEERLVLVASP----------------DHPLAR-----------------------------RAPLVNSLEALLAAVAAG 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 478440705 237 LGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWLKQQC 295
Cdd:COG0583  196 LGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-291 9.99e-27

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: 103.43  E-value: 9.99e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPDYNDQFADCFI---TTNPPerNFVNQFMFTEKLYPVCGKKL 169
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIrygDGDWP--GLEAERLMDEELVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 170 WQQLRnKPLPDSLWQHPLLsvqysdTNESLGDDWLRWCMSGKFELPKDVKINQFSHVLLAAEAARYNLGITLINNYMMDD 249
Cdd:cd08432   80 LAGLP-LLSPADLARHTLL------HDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVAD 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 478440705 250 QDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08432  153 DLAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-65 1.99e-25

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 95.91  E-value: 1.99e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705    6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGE 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 6-282 9.89e-21

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: 89.98  E-value: 9.89e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  86 RHGK---SGNLRLALySSVAVNWLIPK-LEDFRNQHPEIEITLnMVGDQPDYNDQFADC-----FITTNPPERNFVNQFM 156
Cdd:NF040786  83 DRYGkesKGVLRIGA-STIPGQYLLPElLKKFKEKYPNVRFKL-MISDSIKVIELLLEGevdigFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVC--GKKLWQQLRNKPLPDSLWQHPL-LSVQYSDTNESLGDDWLRWCMSgkfelPKDVKInqfshvllAAE-- 231
Cdd:NF040786 161 YKDRLVLITpnGTEKYRMLKEEISISELQKEPFiMREEGSGTRKEAEKALKSLGIS-----LEDLNV--------VASlg 227

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 478440705 232 -------AARYNLGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQP 282
Cdd:NF040786 228 steaikqSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSP 285
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 7-133 5.57e-13

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: 68.02  E-value: 5.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705    7 RALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRqGRSFSLTKVGERYFEEVtNSLGNLSN--ASQM 84
Cdd:TIGR03298   4 RQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHA-RQVRLLEAelLAEL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 478440705   85 IRHGKSGNLRLalysSVAVN------WLIPKLEDFRNQHPeieITLNMVGDQPDY 133
Cdd:TIGR03298  82 PGLAPGAPTRL----TIAVNadslatWFLPALAPVLAREG---VLLDLVVEDQDH 129
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 7-69 4.32e-10

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: 59.37  E-value: 4.32e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478440705   7 RALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFE 69
Cdd:NF041036   4 RYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLE 66
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 2-294 3.51e-58

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 188.51  E-value: 3.51e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   2 KLPPLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNA 81
Cdd:PRK11139   4 RLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  82 SQMIRHGKS-GNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVgDQP-DYNDQFADCFI---TTNPPerNFVNQFM 156
Cdd:PRK11139  84 TRKLRARSAkGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAV-DRLeDFLRDDVDVAIrygRGNWP--GLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVCGKKLWQQlrNKPL--PDSLWQHPLLsvqYSDTNeslgDDWLRWCMSGKFElpkDVKINQ---FSHVLLAAE 231
Cdd:PRK11139 161 LDEYLLPVCSPALLNG--GKPLktPEDLARHTLL---HDDSR----EDWRAWFRAAGLD---DLNVQQgpiFSHSSMALQ 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478440705 232 AARYNLGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWLKQQ 294
Cdd:PRK11139 229 AAIHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAE 291
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-295 1.49e-51

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.05  E-value: 1.49e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   5 PLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQM 84
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  85 IR---HGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNmVGDQPDYNDQFAD-----CFITTNPPERNFVNQFM 156
Cdd:COG0583   82 LRalrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELR-EGNSDRLVDALLEgeldlAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVCGKklwqqlrnkplpdslwQHPLLSvqysdtneslgddwlrwcmsgkfelpkdvKINQFSHVLLAAEAARYN 236
Cdd:COG0583  161 GEERLVLVASP----------------DHPLAR-----------------------------RAPLVNSLEALLAAVAAG 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 478440705 237 LGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWLKQQC 295
Cdd:COG0583  196 LGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-239 3.24e-34

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 126.66  E-value: 3.24e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  86 RHGK-SGNlrLALYS--SVAVNWLIPKLEDFRNQHPEIEITLnMVG-DQPDYNDQFADCFIT-TNPPERNFVNQFMFTEK 160
Cdd:PRK10086  96 KNQElSGT--LTVYSrpSIAQCWLVPRLADFTRRYPSISLTI-LTGnENVNFQRAGIDLAIYfDDAPSAQLTHHFLMDEE 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 161 LYPVCGKKLWQQ--LRNKplPDSLWQHPLLSVQYSDTNESLGDDWLRWCMSGKFELPKDVKINQFSHVLLAAEAARYNLG 238
Cdd:PRK10086 173 ILPVCSPEYAERhaLTGN--PDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLLPPSSGIGFDRSDLAVIAAMNHIG 250


                 .
gi 478440705 239 I 239
Cdd:PRK10086 251 V 251
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-291 9.99e-27

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: 103.43  E-value: 9.99e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPDYNDQFADCFI---TTNPPerNFVNQFMFTEKLYPVCGKKL 169
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIrygDGDWP--GLEAERLMDEELVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 170 WQQLRnKPLPDSLWQHPLLsvqysdTNESLGDDWLRWCMSGKFELPKDVKINQFSHVLLAAEAARYNLGITLINNYMMDD 249
Cdd:cd08432   80 LAGLP-LLSPADLARHTLL------HDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVAD 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 478440705 250 QDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08432  153 DLAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-65 1.99e-25

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 95.91  E-value: 1.99e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705    6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGE 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 93-291 4.95e-21

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: 88.51  E-value: 4.95e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIeiTLNMV-GDQP-DYNDQFADCFITTNPPE-RNFVNQFMFTEKLYPVCGKKL 169
Cdd:cd08481    2 LELAVLPTFGTRWLIPRLPDFLARHPDI--TVNLVtRDEPfDFSQGSFDAAIHFGDPVwPGAESEYLMDEEVVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 170 WQQLRNKPlPDSLWQHPLLsvQYSdTNESLGDDWLRwcMSGkFELPKDVKINQFSHVLLAAEAARYNLGITLINNYMMDD 249
Cdd:cd08481   80 LAGRALAA-PADLAHLPLL--QQT-TRPEAWRDWFE--EVG-LEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEE 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 478440705 250 QDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08481  153 ELARGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 6-282 9.89e-21

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: 89.98  E-value: 9.89e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  86 RHGK---SGNLRLALySSVAVNWLIPK-LEDFRNQHPEIEITLnMVGDQPDYNDQFADC-----FITTNPPERNFVNQFM 156
Cdd:NF040786  83 DRYGkesKGVLRIGA-STIPGQYLLPElLKKFKEKYPNVRFKL-MISDSIKVIELLLEGevdigFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVC--GKKLWQQLRNKPLPDSLWQHPL-LSVQYSDTNESLGDDWLRWCMSgkfelPKDVKInqfshvllAAE-- 231
Cdd:NF040786 161 YKDRLVLITpnGTEKYRMLKEEISISELQKEPFiMREEGSGTRKEAEKALKSLGIS-----LEDLNV--------VASlg 227

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 478440705 232 -------AARYNLGITLINNYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQP 282
Cdd:NF040786 228 steaikqSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSP 285
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-124 3.50e-19

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 85.39  E-value: 3.50e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 478440705  86 rHG----KSGNLRLAL---YSSVAVNWLIpklEDFRNQHPEIEITL 124
Cdd:PRK11242  83 -HDvadlSRGSLRLAMtptFTAYLIGPLI---DAFHARYPGITLTI 124
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-295 1.83e-17

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: 78.87  E-value: 1.83e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   90 SGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLnMVGDQPDYNDQFAD-----CFITTNPPERNFVNQFMFTEKLYPV 164
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELEL-TEGNSEELLDLLLEgeldlAIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  165 CGKKLwQQLRNKPL-PDSLWQHPLLSVqysDTNESLGDDWLRWCMSGKFELPKDVkinQFSHVLLAAEAARYNLGITLIN 243
Cdd:pfam03466  80 APPDH-PLARGEPVsLEDLADEPLILL---PPGSGLRDLLDRALRAAGLRPRVVL---EVNSLEALLQLVAAGLGIALLP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 478440705  244 NYMMDDQDRQQSLVRIPMHELITGDNFYFVYKETRARQPDIMKLGRWLKQQC 295
Cdd:pfam03466 153 RSAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-126 6.65e-17

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 79.22  E-value: 6.65e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   8 ALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEE---VTNSLGNLSNASQM 84
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEarsVIKKMQETRRQCQQ 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 478440705  85 IRHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNM 126
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQ 127
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 6-124 5.90e-16

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 76.35  E-value: 5.90e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 478440705  86 RHGKSGN--LRLALYSSVAVNWLIPKLEDFRNQHPEIEITL 124
Cdd:PRK09906  83 RKIVQEDrqLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIEL 123
PRK09986 PRK09986
LysR family transcriptional regulator;
6-125 2.35e-15

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 74.76  E-value: 2.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNA---S 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSlarV 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 478440705  83 QMIRHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLN 125
Cdd:PRK09986  89 EQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLR 131
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-122 9.94e-15

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 73.13  E-value: 9.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK15421   4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAC 83

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 478440705  86 RHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEI 122
Cdd:PRK15421  84 NEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEM 120
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-125 1.19e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 72.75  E-value: 1.19e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   1 MKLP-PLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGE---RYFEEVTNSLG 76
Cdd:CHL00180   1 TDLPfTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllRYGNRILALCE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 478440705  77 NLSNASQMIRHGKSGNLRLALySSVAVNWLIPKL-EDFRNQHPEIEITLN 125
Cdd:CHL00180  81 ETCRALEDLKNLQRGTLIIGA-SQTTGTYLMPRLiGLFRQRYPQINVQLQ 129
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-133 1.42e-13

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 69.42  E-value: 1.42e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   5 PLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRqGRSFSLTKVGE---RYFEEVtnslgnlsna 81
Cdd:PRK03635   3 DYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQrllRHARQV---------- 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 478440705  82 sQMIRHGKSGNLRLALYS----SVAVN------WLIPKLEDFRNQHPeieITLNMVGDQPDY 133
Cdd:PRK03635  72 -RLLEAELLGELPALDGTpltlSIAVNadslatWFLPALAPVLARSG---VLLDLVVEDQDH 129
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 7-133 5.57e-13

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: 68.02  E-value: 5.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705    7 RALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRqGRSFSLTKVGERYFEEVtNSLGNLSN--ASQM 84
Cdd:TIGR03298   4 RQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHA-RQVRLLEAelLAEL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 478440705   85 IRHGKSGNLRLalysSVAVN------WLIPKLEDFRNQHPeieITLNMVGDQPDY 133
Cdd:TIGR03298  82 PGLAPGAPTRL----TIAVNadslatWFLPALAPVLAREG---VLLDLVVEDQDH 129
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 93-291 5.94e-13

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: 66.24  E-value: 5.94e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITL-------NMVGDQPDYNDQFADcfiTTNPPERNFvnqFMFTEKLYPVC 165
Cdd:cd08484    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLstnnnrvDIAAEGLDFAIRFGE---GAWPGTDAT---RLFEAPLSPLC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 166 GKKLWQQLRNkplPDSLWQHPLLSVQYSdtneslgDDWLRWCMSGKFELPKDVKInQFSHVLLAAEAARYNLGITLINNY 245
Cdd:cd08484   76 TPELARRLSE---PADLANETLLRSYRA-------DEWPQWFEAAGVPPPPINGP-VFDSSLLMVEAALQGAGVALAPPS 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 478440705 246 MMDDQDRQQSLVRiPMHELITGDNFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08484  145 MFSRELASGALVQ-PFKITVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-76 6.05e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 67.91  E-value: 6.05e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 478440705   8 ALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLG 76
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-129 5.45e-12

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 64.84  E-value: 5.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  29 NVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMIRHGK---SGNLRlaLYSSV-AVN 104
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGpslSGELS--LFCSVtAAY 79

                         90       100
                 ....*....|....*....|....*.
gi 478440705 105 WLIPK-LEDFRNQHPEIEITLNmVGD 129
Cdd:PRK11716  80 SHLPPiLDRFRAEHPLVEIKLT-TGD 104
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-130 3.95e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 62.30  E-value: 3.95e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   9 LQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRqGRSFSLTKVGE---RYFEEVtnslgNLSNAS--Q 83
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQrllRHLRQV-----ALLEADllS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 478440705  84 MIRHGKSGNLRLAlyssVAVN------WLIPKLEDFRNQHPE-IEITlnmVGDQ 130
Cdd:PRK13348  81 TLPAERGSPPTLA----IAVNadslatWFLPALAAVLAGERIlLELI---VDDQ 127
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-64 4.34e-11

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 62.35  E-value: 4.34e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 478440705   9 LQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVG 64
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-125 6.43e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 61.93  E-value: 6.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   1 MKLPPLRALQcfEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQG-RSFSLTKVG-------ERYFEEVt 72
Cdd:PRK12682   1 MNLQQLRFVR--EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGkavldviERILREV- 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 478440705  73 nslGNLSNASQMIRHGKSGNLRLALYSSVAvNWLIPK-LEDFRNQHPEIEITLN 125
Cdd:PRK12682  78 ---GNIKRIGDDFSNQDSGTLTIATTHTQA-RYVLPRvVAAFRKRYPKVNLSLH 127
PRK09801 PRK09801
LysR family transcriptional regulator;
4-182 6.98e-11

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.97  E-value: 6.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   4 PPLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFE---EVTNSLGNLSN 80
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEhalEILTQYQRLVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  81 ASQMIRHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPDYNDQFADCFITTNPPERNFVNQFMFTEK 160
Cdd:PRK09801  86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165

                        170       180
                 ....*....|....*....|..
gi 478440705 161 LYPVCGKKLWqqLRNKPLPDSL 182
Cdd:PRK09801 166 KRILCAAPEY--LQKYPQPQSL 185
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 93-291 2.58e-10

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: 58.71  E-value: 2.58e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPDYNDQFADCFI---TTNPPERNfvNQFMFTEKLYPVCGKKL 169
Cdd:cd08487    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIrfgEGLWPATH--NERLLDAPLSVLCSPEI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 170 WQQLRNkplPDSLWQHPLLSvQYSDtneslgDDWLRWCMSGKFElPKDVKINQFSHVLLAAEAARYNLGITLINNYMMDD 249
Cdd:cd08487   80 AKRLSH---PADLINETLLR-SYRT------DEWLQWFEAANMP-PIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSR 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 478440705 250 QDRQQSLVRiPMHELITGDNFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08487  149 EIENGQLVQ-PFKIEVETGSYWLTWLKSKPMTPAMELFRQWI 189
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 7-69 4.32e-10

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: 59.37  E-value: 4.32e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478440705   7 RALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFE 69
Cdd:NF041036   4 RYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLE 66
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 93-291 7.42e-10

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: 57.54  E-value: 7.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITL-------NMVGDQPDYNDQFA-------DCFittnppernfvnqFMFT 158
Cdd:cd08488    2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLstnnnrvDIAAEGLDYAIRFGsgawhgiDAT-------------RLFE 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 159 EKLYPVCGKKLWQQLRNkplPDSLWQHPLLSVQYSdtneslgDDWLRWCMSGkfELPKDVKINQ---FSHVLLAAEAARY 235
Cdd:cd08488   69 APLSPLCTPELARQLRE---PADLARHTLLRSYRA-------DEWPQWFEAA--GVGHPCGLPNsimFDSSLGMMEAALQ 136

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 478440705 236 NLGITLINNYMMDDQDRQQSLVRiPMHELITGDNFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08488  137 GLGVALAPPSMFSRQLASGALVQ-PFATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-132 1.36e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.78  E-value: 1.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 478440705  86 RHGkSGNLRLALYSSVAvNWLIPK-LEDFRNQHPEIEITLNmVGDQPD 132
Cdd:PRK10837  85 RED-NGALRIYASSTIG-NYILPAmIARYRRDYPQLPLELS-VGNSQD 129
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-124 2.50e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 57.36  E-value: 2.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   1 MKLPPLRALQcfEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFS-LTKVGE---RYFEEVTNSLG 76
Cdd:PRK12683   1 MNFQQLRIIR--EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKellQIVERMLLDAE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 478440705  77 NLSNASQMIRHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITL 124
Cdd:PRK12683  79 NLRRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLAL 126
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-122 6.14e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 55.79  E-value: 6.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   9 LQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGER---YFEevtnslgNLSNASQMI 85
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERllpYAE-------TLMNTWQAA 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 478440705  86 RHGKSGNLRLALYS-----SVAVNWLIPKLEDFRNQHPEIEI 122
Cdd:PRK03601  79 KKEVAHTSQHNELSigasaSLWECMLTPWLGRLYQNQEALQF 120
PRK09791 PRK09791
LysR family transcriptional regulator;
6-122 9.23e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.54  E-value: 9.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 478440705  86 --RHGK-SGNLRLALYSSVAVNwLIPK-LEDFRNQHPEIEI 122
Cdd:PRK09791  87 rqRQGQlAGQINIGMGASIARS-LMPAvISRFHQQHPQVKV 126
PRK10341 PRK10341
transcriptional regulator TdcA;
3-144 1.23e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 55.25  E-value: 1.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   3 LPPLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGE---RYFEEVTNSLGNLs 79
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQvllSRSESITREMKNM- 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 478440705  80 nASQMIRHGKSGNLRLAL-YSS-VAVNWLIPKLEDFRNQHPEIEITlnMVGDQ-----PDYNDQFADCFITT 144
Cdd:PRK10341  85 -VNEINGMSSEAVVDVSFgFPSlIGFTFMSDMINKFKEVFPKAQVS--MYEAQlssflPAIRDGRLDFAIGT 153
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-124 2.44e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 54.38  E-value: 2.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFE----------EVTNSL 75
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQgcrrmlhevqDVHEQL 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 478440705  76 GNLSNASqmirhgkSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITL 124
Cdd:PRK10632  84 YAFNNTP-------IGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL 125
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-263 2.62e-08

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 52.99  E-value: 2.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITLnmvgdQPDYNDQFAD---------CFITTNPPERNFVNQFMFTEKLYP 163
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSL-----VEGGSSELLEallegeldlAIVALPVDDPGLESEPLFEEPLVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 164 VCGKK-LWQQLRNKPLPDsLWQHPLLSvqySDTNESLGDDWLRWCMSGKFELPKDVKINQFShvlLAAEAARYNLGITLI 242
Cdd:cd05466   77 VVPPDhPLAKRKSVTLAD-LADEPLIL---FERGSGLRRLLDRAFAEAGFTPNIALEVDSLE---AIKALVAAGLGIALL 149

                        170       180
                 ....*....|....*....|.
gi 478440705 243 NNYMMDDQDRQQsLVRIPMHE 263
Cdd:cd05466  150 PESAVEELADGG-LVVLPLED 169
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-124 2.69e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 54.21  E-value: 2.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   1 MKLPPLRALQcfEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQG-RSFSLTKVGERYFEEVTNSLGNLS 79
Cdd:PRK12684   1 MNLHQLRFVR--EAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERILQEVE 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 478440705  80 NASQMirhGK------SGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITL 124
Cdd:PRK12684  79 NLKRV---GKefaaqdQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSI 126
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 6-123 7.04e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 52.69  E-value: 7.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNR-QGRSFSlTKVGERYFEEVTNS---LGNLSNA 81
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERvRGRLHP-TVQGLRLFEEVQRSyygLDRIVSA 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 478440705  82 SQMIRHGKSGNLRLA---LYSSVavnwLIPKL-EDFRNQHPEIEIT 123
Cdd:PRK11013  85 AESLREFRQGQLSIAclpVFSQS----LLPGLcQPFLARYPDVSLN 126
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
12-165 9.64e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.36  E-value: 9.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  12 FEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMIRHGKSG 91
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  92 NLR---LALYSSVAVNWL------IPKLEDFRNQHPEIEITLNMVGD-QPDYNDQFADcfitTNPPERNFVNQFMFTEKL 161
Cdd:PRK10082  99 AQRkikIAAAHSLSLGLLpsiisqMPPLFTWAIEAIDVDEAVDKLREgQSDCIFSFHD----EDLLEAPFDHIRLFESQL 174


                 ....
gi 478440705 162 YPVC 165
Cdd:PRK10082 175 FPVC 178
PRK12680 PRK12680
LysR family transcriptional regulator;
1-129 1.11e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 52.32  E-value: 1.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   1 MKLPPLRALQCFeAVARLNsFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSF-SLTKVGERYFEEVTNSLGNLS 79
Cdd:PRK12680   1 MTLTQLRYLVAI-ADAELN-ITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEAN 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 478440705  80 N-----ASQmiRHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGD 129
Cdd:PRK12680  79 NirtyaANQ--RRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAE 131
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 3-294 5.78e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 49.99  E-value: 5.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   3 LPPLRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNAS 82
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  83 QMI---RHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPDYNDQFADCFITTNP---PERNFVNQFM 156
Cdd:PRK14997  81 DAIaalQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPrpfEDSDLVMRVL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 157 FTEKLYPVCGKKLWQQLRNKPLPDSLWQHPLLSVqysdtneSLGDDWLRWCMSGKFELPKDVKINQ---FSHVLLAAEAA 233
Cdd:PRK14997 161 ADRGHRLFASPDLIARMGIPSAPAELSHWPGLSL-------ASGKHIHRWELYGPQGARAEVHFTPrmiTTDMLALREAA 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 478440705 234 RYNLGITLINNYMMDDQDRQQSLVRI-----PMHELItgdnfYFVYKETRARQPDIMKLGRWLKQQ 294
Cdd:PRK14997 234 MAGVGLVQLPVLMVKEQLAAGELVAVleewePRREVI-----HAVFPSRRGLLPSVRALVDFLTEE 294
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 100-291 6.86e-07

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: 48.94  E-value: 6.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 100 SVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPDYNDQFADCFITTN--PPERNFVNQFMFTEKLYPVCGKKL--WQQLRN 175
Cdd:cd08482    9 SLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNdaPWPAGMQVIELFPERVGPVCSPSLapTVPLRQ 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 176 KPlPDSLWQHPLLsvqysdTNESLGDDWLRWCMSGKFElPKDVKINQ-FSHVLLAAEAARYNLGITLINNYMMDDQDRQQ 254
Cdd:cd08482   89 AP-AAALLGAPLL------HTRSRPQAWPDWAAAQGLA-PEKLGTGQsFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 478440705 255 SLVrIPMHELITGDnFYFVYKETRARQPDIMKLGRWL 291
Cdd:cd08482  161 RLV-APWGFIETGS-HYVLLRPARLRDSRAGALADWL 195
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 93-125 1.46e-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: 47.72  E-value: 1.46e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 478440705  93 LRLALYSSVAVNWLIPKLEDFRNQHPEIEITLN 125
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLL 34
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-126 1.48e-06

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 48.74  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   1 MKLPPLRALqcFEAVAR-LNsFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFS-LTKVGERYFEEVTNSLGNL 78
Cdd:PRK12681   1 MKLQQLRYI--VEVVNHnLN-VSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKV 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 478440705  79 SN---ASQMIRHGKSGNLRLALYSSVAVNWLIPKLEDFRNQHPeiEITLNM 126
Cdd:PRK12681  78 ESiksVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYP--RVSLHM 126
nhaR PRK11062
transcriptional activator NhaR; Provisional
 12-68 2.30e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 48.08  E-value: 2.30e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 478440705  12 FEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYF 68
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF 68
cbl PRK12679
HTH-type transcriptional regulator Cbl;
13-125 3.98e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 47.50  E-value: 3.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  13 EAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQG-RSFSLTKVGERYF---EEVTNSLGNLSNASQMIRHG 88
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLviaERILNEASNVRRLADLFTND 90

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 478440705  89 KSGNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLN 125
Cdd:PRK12679  91 TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELI 127
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 6-125 1.22e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 45.83  E-value: 1.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNA-SQM 84
Cdd:PRK11233   3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAqLAV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 478440705  85 IRHGK--SGNLRLALYSSVAVNWL-IPKLEDFRNQHPEIEITLN 125
Cdd:PRK11233  83 HNVGQalSGQVSIGLAPGTAASSLtMPLLQAVRAEFPGIVLYLH 126
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 6-124 2.69e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 45.02  E-value: 2.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705   6 LRALQCFEAVARLNSFSKAAEHLNVTQSAVSHQVRLLEDYLGETLFNRQGRSFSLTKVGERYFEEVTNSLGNLSNASQMI 85
Cdd:PRK11151   3 IRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 478440705  86 -RHGK--SGNLRLALYSSVA---VNWLIPKLedfRNQHPEIEITL 124
Cdd:PRK11151  83 sQQGEtmSGPLHIGLIPTVGpylLPHIIPML---HQTFPKLEMYL 124
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-142 1.42e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. 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 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: 176161  Cd Length: 202  Bit Score: 42.11  E-value: 1.42e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 478440705  91 GNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNmVGDQP-DYNDQFADCFI 142
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLG-VSDRPvDLIREGVDCVI 52
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-278 7.35e-04

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: 39.73  E-value: 7.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705  91 GNLRLALYSSVAVNWLIPKLEDFRNQHPEIEITLNMVGDQPD-YNDQFaDCFI-TTNPPERNFVnqfmfteklypvcGKK 168
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDlVEEGF-DLAIrIGELPDSSLV-------------ARR 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478440705 169 LWQQ----------LRNKPLPDS---LWQHPLLSVQYSDTNeslgddwLRWCMSGKfELPKDVKIN---QFSHVLLAAEA 232
Cdd:cd08422   67 LGPVrrvlvaspayLARHGTPQTpedLARHRCLGYRLPGRP-------LRWRFRRG-GGEVEVRVRgrlVVNDGEALRAA 138

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 478440705 233 ARYNLGITLINNYMMDDQDRQQSLVRI-PMHELITGDnFYFVYKETR 278
Cdd:cd08422  139 ALAGLGIALLPDFLVAEDLASGRLVRVlPDWRPPPLP-IYAVYPSRR 184
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
25-79 2.79e-03

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 38.72  E-value: 2.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 478440705  25 AEHLNVTQSAVSHQVRLLEDylgETLFNRQGRSFSLTKVGERYFEEVTNSLGNLS 79
Cdd:COG4742   36 AESLDVSRSTILRQLKELEE---RGLIERDDGEYELTTLGRLVVEEMEPLLDTLE 87
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 95-132 4.28e-03

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176121  Cd Length: 199  Bit Score: 37.56  E-value: 4.28e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 478440705  95 LALYSSV--AVNWLIPKLEDFRNQHPEIEITLNmVGDQPD 132
Cdd:cd08430    2 LSLYCSVtaSYSFLPPILERFRAQHPQVEIKLH-TGDPAD 40
 
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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