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Conserved domains on  [gi|446210261|ref|WP_000288116|]
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DNA-binding transcriptional regulator DsdC [Vibrio cholerae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 10-311 0e+00

D-serine deaminase transcriptional activator; This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. [Regulatory functions, DNA interactions]


:

Pssm-ID: 131091 [Multi-domain]  Cd Length: 302  Bit Score: 598.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   10 KHSRINSFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLN 89
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   90 NLNQEITDIKNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCK 169
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  170 EIFSETIIPVCTPEYAQKYSLTSSMDNLYNTTLLHDNQAWNYNSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAI 249
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNNLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446210261  250 NNAGIAMGRFSLVKSRLSSGELMTPYPNTEVICKQRYYVATLPNKHNQKVKLFIDWLESQVK 311
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQVK 302
 
Name Accession Description Interval E-value
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 10-311 0e+00

D-serine deaminase transcriptional activator; This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. [Regulatory functions, DNA interactions]


Pssm-ID: 131091 [Multi-domain]  Cd Length: 302  Bit Score: 598.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   10 KHSRINSFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLN 89
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   90 NLNQEITDIKNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCK 169
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  170 EIFSETIIPVCTPEYAQKYSLTSSMDNLYNTTLLHDNQAWNYNSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAI 249
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNNLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446210261  250 NNAGIAMGRFSLVKSRLSSGELMTPYPNTEVICKQRYYVATLPNKHNQKVKLFIDWLESQVK 311
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQVK 302
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-314 0e+00

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 568.09  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   4 KDNIFAKHSRINSFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHS 83
Cdd:PRK10086   1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  84 LQKTLNNLNQEITDIKNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMP 163
Cdd:PRK10086  81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 164 DKLSCKEIFSETIIPVCTPEYAQKYSLTSSMDNLYNTTLLHDNQAWNYNSDADEWKTWANANQLENLENISRIGFDRSDL 243
Cdd:PRK10086 161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLLPPSSGIGFDRSDL 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446210261 244 AVIAAINNAGIAMGRFSLVKSRLSSGELMTPYPNTEVICKQRYYVATLPNKHNQKVKLFIDWLESQVKKAV 314
Cdd:PRK10086 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVKTTS 311
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 107-306 2.87e-49

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: 162.75  E-value: 2.87e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 107 LTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYAQ 186
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 187 KYSLTSSMDnLYNTTLLHDNQAWnynsdaDEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVKSRL 266
Cdd:cd08432   82 GLPLLSPAD-LARHTLLHDATRP------EAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDL 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446210261 267 SSGELMTPYPnTEVICKQRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08432  155 AAGRLVRPFD-LPLPSGGAYYLVYPPGRaESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
19-312 4.67e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 4.67e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQEITDI 98
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  99 KN--GETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQG---SGIDVAIYFDDHMPDKLSCKEIFS 173
Cdd:COG0583   83 RAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAlleGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 174 ETIIPVCTPEY--AQKYSLTSSMDNLYNttllhdnqawnynsdadewktwananqlenlenisrigfdrsdlaviAAINN 251
Cdd:COG0583  163 ERLVLVASPDHplARRAPLVNSLEALLA-----------------------------------------------AVAAG 195

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446210261 252 AGIAMGRFSLVKSRLSSGELmTPYPNTEVICKQRYYVATLPNKH-NQKVKLFIDWLESQVKK 312
Cdd:COG0583  196 LGIALLPRFLAADELAAGRL-VALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
19-78 4.66e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 92.45  E-value: 4.66e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQ 78
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
33-84 6.97e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 34.49  E-value: 6.97e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446210261    33 SFSLAADELSLTPSAISHRINKLEEEiGIklferthrkVVLTEEGQRIYHSL 84
Cdd:smart00418  12 CVCELAEILGLSQSTVSHHLKKLREA-GL---------VESRREGKRVYYSL 53
 
Name Accession Description Interval E-value
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 10-311 0e+00

D-serine deaminase transcriptional activator; This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. [Regulatory functions, DNA interactions]


Pssm-ID: 131091 [Multi-domain]  Cd Length: 302  Bit Score: 598.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   10 KHSRINSFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLN 89
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   90 NLNQEITDIKNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCK 169
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  170 EIFSETIIPVCTPEYAQKYSLTSSMDNLYNTTLLHDNQAWNYNSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAI 249
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNNLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446210261  250 NNAGIAMGRFSLVKSRLSSGELMTPYPNTEVICKQRYYVATLPNKHNQKVKLFIDWLESQVK 311
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQVK 302
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-314 0e+00

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 568.09  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   4 KDNIFAKHSRINSFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHS 83
Cdd:PRK10086   1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  84 LQKTLNNLNQEITDIKNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMP 163
Cdd:PRK10086  81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 164 DKLSCKEIFSETIIPVCTPEYAQKYSLTSSMDNLYNTTLLHDNQAWNYNSDADEWKTWANANQLENLENISRIGFDRSDL 243
Cdd:PRK10086 161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLLPPSSGIGFDRSDL 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446210261 244 AVIAAINNAGIAMGRFSLVKSRLSSGELMTPYPNTEVICKQRYYVATLPNKHNQKVKLFIDWLESQVKKAV 314
Cdd:PRK10086 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVKTTS 311
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-312 1.08e-77

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 238.97  E-value: 1.08e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQEITDI 98
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  99 KNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDD-HMP----DKLsckeiFS 173
Cdd:PRK11139  88 RARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRgNWPglrvEKL-----LD 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 174 ETIIPVCTPEYAQKYSLTSSMDNLYNTTLLHDnqawnynSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAG 253
Cdd:PRK11139 163 EYLLPVCSPALLNGGKPLKTPEDLARHTLLHD-------DSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQG 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 254 IAMGRFSLVKSRLSSGELMTPYPnTEVICKQRYYVATLPNKHN-QKVKLFIDWLESQVKK 312
Cdd:PRK11139 236 VALGNRVLAQPEIEAGRLVCPFD-TVLPSPNAFYLVCPDSQAElPKVAAFRQWLLAEAAQ 294
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 107-306 2.87e-49

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: 162.75  E-value: 2.87e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 107 LTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYAQ 186
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 187 KYSLTSSMDnLYNTTLLHDNQAWnynsdaDEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVKSRL 266
Cdd:cd08432   82 GLPLLSPAD-LARHTLLHDATRP------EAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDL 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446210261 267 SSGELMTPYPnTEVICKQRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08432  155 AAGRLVRPFD-LPLPSGGAYYLVYPPGRaESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
19-312 4.67e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 4.67e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQEITDI 98
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  99 KN--GETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQG---SGIDVAIYFDDHMPDKLSCKEIFS 173
Cdd:COG0583   83 RAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAlleGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 174 ETIIPVCTPEY--AQKYSLTSSMDNLYNttllhdnqawnynsdadewktwananqlenlenisrigfdrsdlaviAAINN 251
Cdd:COG0583  163 ERLVLVASPDHplARRAPLVNSLEALLA-----------------------------------------------AVAAG 195

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446210261 252 AGIAMGRFSLVKSRLSSGELmTPYPNTEVICKQRYYVATLPNKH-NQKVKLFIDWLESQVKK 312
Cdd:COG0583  196 LGIALLPRFLAADELAAGRL-VALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLREALAE 256
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 106-306 1.82e-26

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: 103.14  E-value: 1.82e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 106 LLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYA 185
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 186 QKYSLTSSMDnLYNTTLLHdnQAwnynSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAGIA-MGRFsLVKS 264
Cdd:cd08481   81 AGRALAAPAD-LAHLPLLQ--QT----TRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVAlLPRF-LIEE 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 446210261 265 RLSSGELMTPyPNTEVICKQRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08481  153 ELARGRLVVP-FNLPLTSDKAYYLVYPEDKaESPPVQAFRDWL 194
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 106-306 1.96e-26

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: 102.83  E-value: 1.96e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 106 LLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYA 185
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 186 QKysLTSSMDnLYNTTLLHdnqawNYNsdADEWKTWANANQLENLENISRIgFDRSDLAVIAAINNAGIAMGRFSLVKSR 265
Cdd:cd08484   81 RR--LSEPAD-LANETLLR-----SYR--ADEWPQWFEAAGVPPPPINGPV-FDSSLLMVEAALQGAGVALAPPSMFSRE 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446210261 266 LSSGELMTPYPNTevICKQRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08484  150 LASGALVQPFKIT--VSTGSYWLTRLKSKpETPAMSAFSQWL 189
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
19-78 4.66e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 92.45  E-value: 4.66e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQ 78
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 113-306 5.56e-24

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: 96.70  E-value: 5.56e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 113 PSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDH-MPDKLSCKEIFSETIIPVCTPEYAQKYSL- 190
Cdd:cd08482    8 GSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDApWPAGMQVIELFPERVGPVCSPSLAPTVPLr 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 191 TSSMDNLYNTTLLHDnqawnyNSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVKSRLSSGE 270
Cdd:cd08482   88 QAPAAALLGAPLLHT------RSRPQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGR 161

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446210261 271 LMTPYPNTEvicKQRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08482  162 LVAPWGFIE---TGSHYVLLRPARlRDSRAGALADWL 195
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 106-306 1.33e-23

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: 95.30  E-value: 1.33e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 106 LLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYA 185
Cdd:cd08487    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 186 QKysLTSSMDnLYNTTLLHdnqawNYNSdaDEWKTWANANQLENLENISRIgFDRSDLAVIAAINNAGIAMGRFSLVKSR 265
Cdd:cd08487   81 KR--LSHPAD-LINETLLR-----SYRT--DEWLQWFEAANMPPIKIRGPV-FDSSRLMVEAAMQGAGVALAPAKMFSRE 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446210261 266 LSSGELMTPYpNTEVICKqRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08487  150 IENGQLVQPF-KIEVETG-SYWLTWLKSKpMTPAMELFRQWI 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 114-306 4.14e-23

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: 94.14  E-value: 4.14e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 114 SFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYAQKysLTSS 193
Cdd:cd08488    9 TFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELARQ--LREP 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 194 MDnLYNTTLLHDNQawnynsdADEWKTWANANQL-ENLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVKSRLSSGELM 272
Cdd:cd08488   87 AD-LARHTLLRSYR-------ADEWPQWFEAAGVgHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALV 158

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446210261 273 TPYPNTevICKQRYYVATLPNK-HNQKVKLFIDWL 306
Cdd:cd08488  159 QPFATT--LSTGSYWLTRLQSRpETPAMSAFSAWL 191
PRK09801 PRK09801
LysR family transcriptional regulator;
14-197 8.36e-18

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 82.01  E-value: 8.36e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  14 INSFQLSKLHTFEVAARHN-SFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIY-HSLQ--KTLN 89
Cdd:PRK09801   2 LNSWPLAKDLQVLVEIVHSgSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYeHALEilTQYQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  90 NLNQEITDIKNgETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCK 169
Cdd:PRK09801  82 RLVDDVTQIKT-RPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAH 160

                        170       180
                 ....*....|....*....|....*...
gi 446210261 170 EIFSETIIPVCTPEYAQKYSLTSSMDNL 197
Cdd:PRK09801 161 LLTKNKRILCAAPEYLQKYPQPQSLQEL 188
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-306 1.16e-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: 79.64  E-value: 1.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  104 SGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQG--SG-IDVAIYFDDHMPDKLSCKEIFSETIIPVC 180
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLllEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  181 TPEY--AQKYSLTssMDNLYNTTLLHdnqawnYNSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMGR 258
Cdd:pfam03466  81 PPDHplARGEPVS--LEDLADEPLIL------LPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 446210261  259 FSLVKSRLSSGELMT-PYPNTEVicKQRYYVATLPNKHNQ-KVKLFIDWL 306
Cdd:pfam03466 153 RSAVARELADGRLVAlPLPEPPL--PRELYLVWRKGRPLSpAVRAFIEFL 200
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 22-78 2.77e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 71.90  E-value: 2.77e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446210261  22 LHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQ 78
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
43-171 5.70e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 70.62  E-value: 5.70e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  43 LTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNN---LNQEITDiKNGETSGLLTIYSRPSFAQCW 119
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQwqqLRHTLDQ-QGPSLSGELSLFCSVTAAYSH 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446210261 120 LVPRIHAFKELYPSIDLKLLTGN-----ENIsfQGSGIDVAIY-FDDHMPDKLSCKEI 171
Cdd:PRK11716  82 LPPILDRFRAEHPLVEIKLTTGDaadavEKV--QSGEADLAIAaKPETLPASVAFSPI 137
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 19-175 9.90e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 70.37  E-value: 9.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLN---QEI 95
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagrRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  96 TDIKNgETSGLLTIYSRPSFAqCWLV-PRIHAFKELYPSIDLK-----------LLTGNEnisfqgsgIDVAIYFDD-HM 162
Cdd:PRK11242  83 HDVAD-LSRGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTiremsqerieaLLADDE--------LDVGIAFAPvHS 152

                        170
                 ....*....|...
gi 446210261 163 PDkLSCKEIFSET 175
Cdd:PRK11242 153 PE-IEAQPLFTET 164
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 105-306 3.54e-13

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: 67.08  E-value: 3.54e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 105 GLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEY 184
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 185 AQKYSLTSSMDNLYNTTLLHdnqaWNYNSDADEWkTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVKS 264
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLG----YRLPGRPLRW-RFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 446210261 265 RLSSGEL---MTPYPNTEVIckqrYYVATLPNKHN-QKVKLFIDWL 306
Cdd:cd08422  156 DLASGRLvrvLPDWRPPPLP----IYAVYPSRRHLpAKVRAFIDFL 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 31-156 1.11e-12

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 67.32  E-value: 1.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  31 HNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTL--NNLNQEITDIKNGETSGLLT 108
Cdd:PRK14997  16 EGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveAQAAQDAIAALQVEPRGIVK 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446210261 109 IYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAI 156
Cdd:PRK14997  96 LTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAI 143
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
22-78 1.51e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.75  E-value: 1.51e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446210261  22 LHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQ 78
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGE 63
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-142 2.06e-12

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 66.54  E-value: 2.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  21 KLHTF----EVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVV-LTEEGQRIYHSLQKTLnnlnQEI 95
Cdd:PRK12684   2 NLHQLrfvrEAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERIL----QEV 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446210261  96 TDIK------NGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGN 142
Cdd:PRK12684  78 ENLKrvgkefAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGS 130
rbcR CHL00180
LysR transcriptional regulator; Provisional
 16-138 2.55e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 2.55e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  16 SFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLnNLNQE- 94
Cdd:CHL00180   4 PFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL-ALCEEt 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446210261  95 ---ITDIKNGEtSGLLTIYSRPSFAQcWLVPRIHA-FKELYPSIDLKL 138
Cdd:CHL00180  83 craLEDLKNLQ-RGTLIIGASQTTGT-YLMPRLIGlFRQRYPQINVQL 128
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 107-306 2.72e-12

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: 64.29  E-value: 2.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 107 LTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEYAQ 186
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 187 KysltSSMDNLYNTTLLHdnqaWNYNSDADEWKTWANANQLEnLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVKSRL 266
Cdd:cd08483   82 D----RKVDSLADLAGLP----WLQERGTNEQRVWLASMGVV-PDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDI 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446210261 267 SSGELMTPYPNTEVicKQRYYVATLPNKHNQKVKLFIDWL 306
Cdd:cd08483  153 AAGRLTVLFEEEEE--GLGYHIVTRPGVLRPAAKAFVRWL 190
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 21-138 6.47e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 65.01  E-value: 6.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  21 KLHTFEV---AARHN-SFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVV-LTEEGQRIYHSLQKTLNNLNQ-- 93
Cdd:PRK12682   2 NLQQLRFvreAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNik 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446210261  94 EITDIKNGETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKL 138
Cdd:PRK12682  82 RIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSL 126
cbl PRK12679
HTH-type transcriptional regulator Cbl;
26-156 4.10e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 62.90  E-value: 4.10e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  26 EVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVV-LTEEGQRIYHSLQKTLNNLN--QEITDIKNGE 102
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASnvRRLADLFTND 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446210261 103 TSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGN--ENIS-FQGSGIDVAI 156
Cdd:PRK12679  91 TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTpqEIATlLQNGEADIGI 147
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
32-156 4.46e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 62.47  E-value: 4.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  32 NSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQ--EITDIKNGETSGLLTI 109
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDvhEQLYAFNNTPIGTLRI 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446210261 110 YSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAI 156
Cdd:PRK10632  97 GCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVI 143
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
22-81 1.67e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 57.67  E-value: 1.67e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  22 LHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERThRKVVLTEEGQRIY 81
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLL 65
PRK09986 PRK09986
LysR family transcriptional regulator;
9-138 4.39e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.65  E-value: 4.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261   9 AKHSRINsfqLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTL 88
Cdd:PRK09986   2 ERLYRID---LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446210261  89 NNLNQ---EITDIKNGETSGL-LTIYSRPSFAQcwLVPRIHAFKELYPSIDLKL 138
Cdd:PRK09986  79 DNAEQslaRVEQIGRGEAGRIeIGIVGTALWGR--LRPAMRHFLKENPNVEWLL 130
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 29-138 5.06e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 56.58  E-value: 5.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  29 ARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLN--QEITDIKNGETSGL 106
Cdd:PRK11151  13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKvlKEMASQQGETMSGP 92

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446210261 107 LTIYSRPSFAQcWLVPRI-HAFKELYPSIDLKL 138
Cdd:PRK11151  93 LHIGLIPTVGP-YLLPHIiPMLHQTFPKLEMYL 124
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 19-142 7.17e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 7.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYhslQKTLNNLNQ--EIT 96
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY---PRALALLEQavEIE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446210261  97 DIKNGEtSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGN 142
Cdd:PRK10837  82 QLFRED-NGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGN 126
PRK09791 PRK09791
LysR family transcriptional regulator;
16-141 1.33e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.15  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  16 SFQLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQEI 95
Cdd:PRK09791   4 QVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQ 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446210261  96 TDIKN--GETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTG 141
Cdd:PRK09791  84 EDIRQrqGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEG 131
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
22-80 3.37e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.01  E-value: 3.37e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446210261  22 LHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERThRKVVLTEEGQRI 80
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRL 64
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
23-203 4.85e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 53.48  E-value: 4.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  23 HTFEVAARHNSFSLAADELSL--TPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQEITDIKN 100
Cdd:PRK15421   6 HLKTLQALRNCGSLAAAAATLhqTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 101 GETSGLLTIYSRPSFAQcWLVPRIHAFKELYPSIDLKLLTG---NENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETII 177
Cdd:PRK15421  86 PQQTRLRIAIECHSCIQ-WLTPALENFHKNWPQVEMDFKSGvtfDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVR 164

                        170       180
                 ....*....|....*....|....*...
gi 446210261 178 PVCTPEY--AQKYSLTSsmDNLYNTTLL 203
Cdd:PRK15421 165 LVLAPDHplAAKTRITP--EDLASETLL 190
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 28-138 7.35e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.74  E-value: 7.35e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  28 AARHNsFSL--AADELSLTPSAISHRINKLEEEIGIKLFERTHRKVV-LTEEGQRIYHSLQKTL---NNLNQeITDIKNG 101
Cdd:PRK12683  12 AVRQN-FNLteVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLldaENLRR-LAEQFAD 89

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446210261 102 ETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKL 138
Cdd:PRK12683  90 RDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLAL 126
PRK10341 PRK10341
transcriptional regulator TdcA;
14-133 1.75e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.79  E-value: 1.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  14 INSFQLSK---LHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNN 90
Cdd:PRK10341   1 MSTILLPKtqhLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446210261  91 LNQEITDIkNGETSGLLTIYS--RPSFAQCWLVPR-IHAFKELYPS 133
Cdd:PRK10341  81 MKNMVNEI-NGMSSEAVVDVSfgFPSLIGFTFMSDmINKFKEVFPK 125
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 18-177 4.49e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.54  E-value: 4.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  18 QLSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNL-NQEIT 96
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAeKAKLR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  97 DIKNGETSGLLTIYSRPSfAQCWLVPR-IHAFKELYPSIDLKLL----TGNENISFQGSgIDVAIYFDDHMPDKLSCKEI 171
Cdd:PRK09906  82 ARKIVQEDRQLTIGFVPS-AEVNLLPKvLPMFRLRHPDTLIELVslitTQQEEKLRRGE-LDVGFMRHPVYSDEIDYLEL 159


                 ....*.
gi 446210261 172 FSETII 177
Cdd:PRK09906 160 LDEPLV 165
nhaR PRK11062
transcriptional activator NhaR; Provisional
 37-100 4.50e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 50.39  E-value: 4.50e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446210261  37 AADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLnNLNQEITDIKN 100
Cdd:PRK11062  24 AAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMF-TLSQEMLDIVN 86
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
22-122 1.30e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 48.86  E-value: 1.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  22 LHTF-EVA-ARHnsFSLAADELSLTPSAISHRINKLEEEIGIKLFERtHR-KVVLTEEGQRI--Y-HSLQKTLNNLNQEI 95
Cdd:PRK03601   6 LKTFlEVSrTRH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTR-HRnNIRLTAAGERLlpYaETLMNTWQAAKKEV 82

                         90       100
                 ....*....|....*....|....*..
gi 446210261  96 TdikNGETSGLLTIYSRPSFAQCWLVP 122
Cdd:PRK03601  83 A---HTSQHNELSIGASASLWECMLTP 106
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 107-306 1.76e-06

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: 47.59  E-value: 1.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 107 LTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQG--SG-IDVAIYFDDHMPDKLSCKEIFSETIIPVCTPE 183
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEAllEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 184 YAQKYSLTSSMDNLYNTTLLHdnqawnYNSDADEWKTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMGRFSLVK 263
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLIL------FERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446210261 264 SRLSSGelMTPYPNTEVICKQRYYVATLPNKH-NQKVKLFIDWL 306
Cdd:cd05466  156 ELADGG--LVVLPLEDPPLSRTIGLVWRKGRYlSPAARAFLELL 197
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
22-202 2.42e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.13  E-value: 2.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  22 LHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGqRIYHS-LQKTLNNLNQEITDIKN 100
Cdd:PRK10082  16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQG-KIFHSqIRHLLQQLESNLAELRG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 101 GE---------------TSGLL-TIYSR--PSFAqcWLVPRIhafkELYPSIDlKLLTGNENISFQGSGIDVAIYFDDHM 162
Cdd:PRK10082  95 GSdyaqrkikiaaahslSLGLLpSIISQmpPLFT--WAIEAI----DVDEAVD-KLREGQSDCIFSFHDEDLLEAPFDHI 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446210261 163 pdklsckEIFSETIIPVCTPE--------YAQ------KYSLTSSMDNLYNTTL 202
Cdd:PRK10082 168 -------RLFESQLFPVCASDehgealfnLAQphfpllNYSRNSYMGRLINRTL 214
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 33-181 2.43e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 48.14  E-value: 2.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  33 SFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLNNLNQEITDIKN-GET-SGLLTIY 110
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNvGQAlSGQVSIG 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446210261 111 SRP-SFAQCWLVPRIHAFKELYPSIDLKLltgNENISFQGSG------IDVAIYFDDHMPDKLSCKEIFSETIIPVCT 181
Cdd:PRK11233  97 LAPgTAASSLTMPLLQAVRAEFPGIVLYL---HENSGATLNEklmngqLDMAVIYEHSPVAGLSSQPLLKEDLFLVGT 171
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 103-203 3.87e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 46.56  E-value: 3.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 103 TSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTP 182
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                         90       100
                 ....*....|....*....|.
gi 446210261 183 EYAQKYSLTSSMDNLYNTTLL 203
Cdd:cd08478   81 DYLARHGTPQSIEDLAQHQLL 101
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 19-109 7.80e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.56  E-value: 7.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  19 LSKLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKTLnNLNQE-ITD 97
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL-RFNDEaCSS 91

                         90
                 ....*....|..
gi 446210261  98 IKNGETSGLLTI 109
Cdd:PRK15092  92 LMYSNLQGVLTI 103
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-307 1.16e-05

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: 45.20  E-value: 1.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 105 GLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFdDHMPDK-LSCKEIFSETIIPVCTPE 183
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRV-GELADSsLVARRLGELRMVTCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 184 YAQKYSLTSSMDNlynttlLHDNQAWNY----NSDADEWkTWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMG-R 258
Cdd:cd08472   80 YLARHGTPRHPED------LERHRAVGYfsarTGRVLPW-EFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVpR 152

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446210261 259 FsLVKSRLSSGELM--------TPYPntevickqrYYVATLPNKH-NQKVKLFIDWLE 307
Cdd:cd08472  153 F-MVRPHLASGRLVevlpdwrpPPLP---------VSLLYPHRRHlSPRVRVFVDWVA 200
PRK12680 PRK12680
LysR family transcriptional regulator;
35-156 3.96e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 44.61  E-value: 3.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  35 SLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKV-VLTEEGQRIYHSLQKTLNNLNQEITDIKNG--ETSGLLTIYS 111
Cdd:PRK12680  20 TLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQrrESQGQLTLTT 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446210261 112 RPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISF----QGsGIDVAI 156
Cdd:PRK12680 100 THTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALdllgQG-DADIAI 147
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
38-97 1.23e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 41.49  E-value: 1.23e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446210261  38 ADELSLTPSAISHRINKLEEEigiKLFERTH-------RKVVLTEEGQRIYHSLQKTLNNLNQEITD 97
Cdd:COG1846   59 AERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAELLA 122
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
21-152 1.60e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 42.73  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  21 KLHTFEVAARHNSFSLAADELSLTPSAISHRINKLEEEIGIKLFERTHRKVVLTEEGQRIYHSLQKT---LNNLNQEITd 97
Cdd:PRK15243   8 KLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHyifLHALEQEIG- 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446210261  98 iKNGETSGLLTIysrpsfaqcwlvprihaFKELYPSIDLKLLTGNENISFQGSGI 152
Cdd:PRK15243  87 -PTGKTKQLEII-----------------FDEIYPESLKNLIISALTISGQKTNI 123
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-218 2.95e-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 10. 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: 176169  Cd Length: 198  Bit Score: 41.17  E-value: 2.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 105 GLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEY 184
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446210261 185 AQKYSLTSSMDNLynttLLHDNQAWNYNSDADEW 218
Cdd:cd08480   81 LARHGTPLTPQDL----ARHNCLGFNFRRALPDW 110
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-271 3.12e-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 4. 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: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 41.00  E-value: 3.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 104 SGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIY--FDDHMPDKLSCKEIFSETIIPVCT 181
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRvrFPPLEDSSLVMRVLGQSRQRLVAS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 182 PEYAQKYSLTSSMDNLynttLLHDNQAWNYNSDADEWKTWANANQLENLENISRIGFDrsDLAVI--AAINNAGIAMGRF 259
Cdd:cd08473   82 PALLARLGRPRSPEDL----AGLPTLSLGDVDGRHSWRLEGPDGESITVRHRPRLVTD--DLLTLrqAALAGVGIALLPD 155

                        170
                 ....*....|..
gi 446210261 260 SLVKSRLSSGEL 271
Cdd:cd08473  156 HLCREALRAGRL 167
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-306 4.98e-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 9. 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: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 40.27  E-value: 4.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 105 GLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFDDHMPDKLSCKEIFSETIIPVCTPEY 184
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 185 AQKYSLTSSMDNL--YNTTLLHDNqawnyNSDADEWKtWANANQLENLENISRIGFDRSDLAVIAAINNAGIAMgRfSL- 261
Cdd:cd08479   81 LERHGAPASPEDLarHDCLVIREN-----DEDFGLWR-LRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIIL-R-SEw 152

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446210261 262 -VKSRLSSGELMT-----PYPNTEVickqryyVATLPNKHNQ--KVKLFIDWL 306
Cdd:cd08479  153 dVAPYLRSGRLVRvlpdwQLPDADI-------WAVYPSRLSRsaRVRVFVDFL 198
cysB PRK12681
HTH-type transcriptional regulator CysB;
26-136 7.07e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 40.65  E-value: 7.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  26 EVAaRHN-SFSLAADELSLTPSAISHRINKLEEEIGIKLFERT--HRKVVlTEEGQRIYHSLQKTLNNLN------QEIT 96
Cdd:PRK12681  11 EVV-NHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSgkHLTQV-TPAGEEIIRIAREILSKVEsiksvaGEHT 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446210261  97 DikngETSGLLTIYSRPSFAQCWLVPRIHAFKELYPSIDL 136
Cdd:PRK12681  89 W----PDKGSLYIATTHTQARYALPPVIKGFIERYPRVSL 124
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 48-140 7.44e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.75  E-value: 7.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261  48 ISHRINKLEEEIGIKLFERTHRKVVLT-------EEGQRIYHSLQKtLNNLNQEITDIKNGEtsglLTIYSRPSFAQCWL 120
Cdd:PRK11013  35 VSRELARFEKVIGLKLFERVRGRLHPTvqglrlfEEVQRSYYGLDR-IVSAAESLREFRQGQ----LSIACLPVFSQSLL 109

                         90       100
                 ....*....|....*....|
gi 446210261 121 VPRIHAFKELYPSIDLKLLT 140
Cdd:PRK11013 110 PGLCQPFLARYPDVSLNIVP 129
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
33-84 6.97e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 34.49  E-value: 6.97e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446210261    33 SFSLAADELSLTPSAISHRINKLEEEiGIklferthrkVVLTEEGQRIYHSL 84
Cdd:smart00418  12 CVCELAEILGLSQSTVSHHLKKLREA-GL---------VESRREGKRVYYSL 53
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-164 7.62e-03

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 2. 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: 176160  Cd Length: 201  Bit Score: 37.12  E-value: 7.62e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446210261 105 GLLTIYSRPSFAQCWLVPRIHAFKELYPSIDLKLLTGNENISFQGSGIDVAIYFdDHMPD 164
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRI-GHLPD 59
 
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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