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Conserved domains on  [gi|2058454114|gb|QXA40272|]
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DNA-binding transcriptional regulator DsdC [Escherichia coli]

Protein Classification

DNA-binding transcriptional regulator DsdC( domain architecture ID 11484572)

DNA-binding transcriptional regulator DsdC regulates the expression of the dsdX-dsdA operon

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-309 0e+00

DNA-binding transcriptional regulator DsdC;


:

Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 640.51  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114   2 EPLREIRNRLLNGWQLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWA 81
Cdd:PRK10086    1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  82 LKSSLDTLNQEILDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPS 161
Cdd:PRK10086   81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 162 AQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLSHCTLLHDRQAWSNDSGTDEWHSWAQHYAVNL-PTSSGIGFDRSDL 240
Cdd:PRK10086  161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLlPPSSGIGFDRSDL 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2058454114 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHYYITTLPGRQWPKIEAFITWLREQVCQ 309
Cdd:PRK10086  241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVKT 309
 
Name Accession Description Interval E-value
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-309 0e+00

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 640.51  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114   2 EPLREIRNRLLNGWQLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWA 81
Cdd:PRK10086    1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  82 LKSSLDTLNQEILDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPS 161
Cdd:PRK10086   81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 162 AQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLSHCTLLHDRQAWSNDSGTDEWHSWAQHYAVNL-PTSSGIGFDRSDL 240
Cdd:PRK10086  161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLlPPSSGIGFDRSDL 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2058454114 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHYYITTLPGRQWPKIEAFITWLREQVCQ 309
Cdd:PRK10086  241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVKT 309
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 8-307 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: 598.81  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114   8 RNRLLNGWQLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLD 87
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  88 TLNQEILDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHH 167
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 168 FLMDEEILPVCSPEYAQRHDLTNTVINLSHCTLLHDRQAWSNDSGTDEWHSWAQHYAVN-LPTSSGIGFDRSDLAVIAAM 246
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNnLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2058454114 247 NHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHYYITTLPGRQWPKIEAFITWLREQV 307
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQV 301
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 104-303 1.34e-58

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: 186.63  E-value: 1.34e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 104 TLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYA 183
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 184 QRHDLTnTVINLSHCTLLHDRQAWsndsgtDEWHSWAQH-YAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKR 262
Cdd:cd08432    81 AGLPLL-SPADLARHTLLHDATRP------EAWQWWLWAaGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADD 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2058454114 263 LASGELVAPFgDMTVKCHQHYYITTLPGR-QWPKIEAFITWL 303
Cdd:cd08432   154 LAAGRLVRPF-DLPLPSGGAYYLVYPPGRaESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
17-309 1.08e-51

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 1.08e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVY-WALK--SSLDTLNQEI 93
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLeRARRilAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  94 LDIKnQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNV---NLQRAGIDLAIYFDDAPSAQLTHHFLM 170
Cdd:COG0583    83 RALR-GGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 171 DEEILPVCSPEyaqrhdltntvinlshctllhdrqawsndsgtdewHSWAQHYAVnlptssgigFDRSDLAVIAAMNHIG 250
Cdd:COG0583   162 EERLVLVASPD-----------------------------------HPLARRAPL---------VNSLEALLAAVAAGLG 197

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2058454114 251 VAMGRKRLVQKRLASGELVA-PFGDMTVkcHQHYYITTLPGRQW-PKIEAFITWLREQVCQ 309
Cdd:COG0583   198 IALLPRFLAADELAAGRLVAlPLPDPPP--PRPLYLVWRRRRHLsPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
17-76 1.06e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.98  E-value: 1.06e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGK 76
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 17-305 1.77e-18

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 83.82  E-value: 1.77e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDI 96
Cdd:NF040786    3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  97 KN--QELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVL-TGNDNV--NLQRAGIDLAIYFDDAPSAQLTHHFLMD 171
Cdd:NF040786   83 DRygKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMiSDSIKVieLLLEGEVDIGFTGTKLEKKRLVYTPFYK 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 172 EEILPVCSPEYAQRHdLTNTVINLSHCTllhdRQAW---SNDSGTdeWHSwAQHYAVNLptssgiGFDRSDLAVIAAMNH 248
Cdd:NF040786  163 DRLVLITPNGTEKYR-MLKEEISISELQ----KEPFimrEEGSGT--RKE-AEKALKSL------GISLEDLNVVASLGS 228

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 249 -----------IGVAMGRKRLVQKRLASGE-LVAPFGDMTVKchQHYYITTLPGRQWPK-IEAFITWLRE 305
Cdd:NF040786  229 teaikqsveagLGISVISELAAEKEVERGRvLIFPIPGLPKN--RDFYLVYNKNRQLSPtAEAFLQFVKE 296
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
36-85 1.43e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 36.42  E-value: 1.43e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2058454114   36 AEELSLSPSAVSHRINQLEEElGIqlfVRSHRkvelthEGKRVYWALKSS 85
Cdd:smart00418  17 AEILGLSQSTVSHHLKKLREA-GL---VESRR------EGKRVYYSLTDE 56
 
Name Accession Description Interval E-value
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-309 0e+00

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 640.51  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114   2 EPLREIRNRLLNGWQLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWA 81
Cdd:PRK10086    1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  82 LKSSLDTLNQEILDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPS 161
Cdd:PRK10086   81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 162 AQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLSHCTLLHDRQAWSNDSGTDEWHSWAQHYAVNL-PTSSGIGFDRSDL 240
Cdd:PRK10086  161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLlPPSSGIGFDRSDL 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2058454114 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHYYITTLPGRQWPKIEAFITWLREQVCQ 309
Cdd:PRK10086  241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVKT 309
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 8-307 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: 598.81  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114   8 RNRLLNGWQLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLD 87
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  88 TLNQEILDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHH 167
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 168 FLMDEEILPVCSPEYAQRHDLTNTVINLSHCTLLHDRQAWSNDSGTDEWHSWAQHYAVN-LPTSSGIGFDRSDLAVIAAM 246
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNnLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2058454114 247 NHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHYYITTLPGRQWPKIEAFITWLREQV 307
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQV 301
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-307 3.28e-72

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 225.11  E-value: 3.28e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDI 96
Cdd:PRK11139    8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  97 KNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILP 176
Cdd:PRK11139   88 RARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLP 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 177 VCSPEYAQRHDLTNTVINLSHCTLLHdrqawsnDSGTDEWHSWAQHYAV-NLPTSSGIGFDRSDLAVIAAMNHIGVAMGR 255
Cdd:PRK11139  168 VCSPALLNGGKPLKTPEDLARHTLLH-------DDSREDWRAWFRAAGLdDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2058454114 256 KRLVQKRLASGELVAPFgDMTVKCHQHYYITTLPGR-QWPKIEAFITWLREQV 307
Cdd:PRK11139  241 RVLAQPEIEAGRLVCPF-DTVLPSPNAFYLVCPDSQaELPKVAAFRQWLLAEA 292
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 104-303 1.34e-58

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: 186.63  E-value: 1.34e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 104 TLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYA 183
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 184 QRHDLTnTVINLSHCTLLHDRQAWsndsgtDEWHSWAQH-YAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKR 262
Cdd:cd08432    81 AGLPLL-SPADLARHTLLHDATRP------EAWQWWLWAaGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADD 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2058454114 263 LASGELVAPFgDMTVKCHQHYYITTLPGR-QWPKIEAFITWL 303
Cdd:cd08432   154 LAAGRLVRPF-DLPLPSGGAYYLVYPPGRaESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
17-309 1.08e-51

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 1.08e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVY-WALK--SSLDTLNQEI 93
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLeRARRilAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  94 LDIKnQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNV---NLQRAGIDLAIYFDDAPSAQLTHHFLM 170
Cdd:COG0583    83 RALR-GGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 171 DEEILPVCSPEyaqrhdltntvinlshctllhdrqawsndsgtdewHSWAQHYAVnlptssgigFDRSDLAVIAAMNHIG 250
Cdd:COG0583   162 EERLVLVASPD-----------------------------------HPLARRAPL---------VNSLEALLAAVAAGLG 197

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2058454114 251 VAMGRKRLVQKRLASGELVA-PFGDMTVkcHQHYYITTLPGRQW-PKIEAFITWLREQVCQ 309
Cdd:COG0583   198 IALLPRFLAADELAAGRLVAlPLPDPPP--PRPLYLVWRRRRHLsPAVRAFLDFLREALAE 256
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 104-303 3.23e-35

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: 126.26  E-value: 3.23e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 104 TLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYA 183
Cdd:cd08481     1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 184 QRHDLtNTVINLSHCTLLHdrQAwsndSGTDEWHSWAQHYAVNLP-TSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKR 262
Cdd:cd08481    81 AGRAL-AAPADLAHLPLLQ--QT----TRPEAWRDWFEEVGLEVPtAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEE 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2058454114 263 LASGELVAPFgDMTVKCHQHYYITTLPGR-QWPKIEAFITWL 303
Cdd:cd08481   154 LARGRLVVPF-NLPLTSDKAYYLVYPEDKaESPPVQAFRDWL 194
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 114-303 2.55e-28

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: 107.84  E-value: 2.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 114 AQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQR----HDLT 189
Cdd:cd08484    11 AVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPELARRlsepADLA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 190 NTvinlshcTLLHDRQawsndsgTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELV 269
Cdd:cd08484    91 NE-------TLLRSYR-------ADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALV 156

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2058454114 270 APFgDMTVKCHQhYYITTLPGRQW-PKIEAFITWL 303
Cdd:cd08484   157 QPF-KITVSTGS-YWLTRLKSKPEtPAMSAFSQWL 189
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 105-303 4.96e-27

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: 104.79  E-value: 4.96e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 105 LTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHF-LMDEEILPVCSPEYA 183
Cdd:cd08482     2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPAGMQVIeLFPERVGPVCSPSLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 184 QR-HDLTNTVINLSHCTLLHDRqawsndSGTDEWHSWAQHYAVN-LPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQK 261
Cdd:cd08482    82 PTvPLRQAPAAALLGAPLLHTR------SRPQAWPDWAAAQGLApEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRD 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2058454114 262 RLASGELVAPFGDMTVKchQHYYITTLPGRQWPKIEAFITWL 303
Cdd:cd08482   156 DLASGRLVAPWGFIETG--SHYVLLRPARLRDSRAGALADWL 195
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 117-303 9.15e-24

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: 96.06  E-value: 9.15e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 117 WLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRhdlTNTVINLS 196
Cdd:cd08488    14 WLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELARQ---LREPADLA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 197 HCTLLHDRQAwsndsgtDEWHSWAQHYAV--NLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELVAPFgD 274
Cdd:cd08488    91 RHTLLRSYRA-------DEWPQWFEAAGVghPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQPF-A 162

                         170       180       190
                  ....*....|....*....|....*....|
gi 2058454114 275 MTVKCHQhYYITTLPGR-QWPKIEAFITWL 303
Cdd:cd08488   163 TTLSTGS-YWLTRLQSRpETPAMSAFSAWL 191
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 105-303 1.76e-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: 1.76e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 105 LTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQ 184
Cdd:cd08487     2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIAK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 185 R----HDLTNTvinlshcTLLHDRQawsndsgTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQ 260
Cdd:cd08487    82 RlshpADLINE-------TLLRSYR-------TDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFS 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2058454114 261 KRLASGELVAPFgDMTVKCHQhYYITTLPGRQW-PKIEAFITWL 303
Cdd:cd08487   148 REIENGQLVQPF-KIEVETGS-YWLTWLKSKPMtPAMELFRQWI 189
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
17-76 1.06e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.98  E-value: 1.06e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGK 76
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-306 5.01e-21

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: 88.89  E-value: 5.01e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 102 SGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDN--VNLQRAG-IDLAIYFDDAPSAQLTHHFLMDEEILPVC 178
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 179 SPEYAQRHDLTNTVINLSHCTLLHDRqawSNDSGTDEWHSWAQHYAVNLptSSGIGFDRSDLAVIAAMNHIGVAMGRKRL 258
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLP---PGSGLRDLLDRALRAAGLRP--RVVLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2058454114 259 VQKRLASGELVA-PFGDMTVkcHQHYYITTLPGR-QWPKIEAFITWLREQ 306
Cdd:pfam03466 156 VARELADGRLVAlPLPEPPL--PRELYLVWRKGRpLSPAVRAFIEFLREA 203
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 105-303 3.49e-20

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: 86.24  E-value: 3.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 105 LTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYF--DDAPSAQLThhFLMDEEILPVCSPEY 182
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYgnGDWPGLESE--PLTAAPFVVVAAPGL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 183 -AQRhdltnTVINLSHCTLLHdrqaWSNDSGTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQK 261
Cdd:cd08483    80 lGDR-----KVDSLADLAGLP----WLQERGTNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEP 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2058454114 262 RLASGELVAPFGDMTVKchQHYYITTLPGRQWPKIEAFITWL 303
Cdd:cd08483   151 DIAAGRLTVLFEEEEEG--LGYHIVTRPGVLRPAAKAFVRWL 190
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 103-303 7.03e-19

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: 82.87  E-value: 7.03e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 103 GTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEY 182
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 183 AQRHDLTNTVINLSHctllHDRQAWSNDSGTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKR 262
Cdd:cd08422    81 LARHGTPQTPEDLAR----HRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2058454114 263 LASGELVAPFGDMTVKCHQHYYITtlPGRQW--PKIEAFITWL 303
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVY--PSRRHlpAKVRAFIDFL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 17-305 1.77e-18

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 83.82  E-value: 1.77e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDI 96
Cdd:NF040786    3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  97 KN--QELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVL-TGNDNV--NLQRAGIDLAIYFDDAPSAQLTHHFLMD 171
Cdd:NF040786   83 DRygKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMiSDSIKVieLLLEGEVDIGFTGTKLEKKRLVYTPFYK 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 172 EEILPVCSPEYAQRHdLTNTVINLSHCTllhdRQAW---SNDSGTdeWHSwAQHYAVNLptssgiGFDRSDLAVIAAMNH 248
Cdd:NF040786  163 DRLVLITPNGTEKYR-MLKEEISISELQ----KEPFimrEEGSGT--RKE-AEKALKSL------GISLEDLNVVASLGS 228

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 249 -----------IGVAMGRKRLVQKRLASGE-LVAPFGDMTVKchQHYYITTLPGRQWPK-IEAFITWLRE 305
Cdd:NF040786  229 teaikqsveagLGISVISELAAEKEVERGRvLIFPIPGLPKN--RDFYLVYNKNRQLSPtAEAFLQFVKE 296
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 17-189 1.49e-17

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 81.16  E-value: 1.49e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGkRVYW-----ALKsSLDTLNQ 91
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAG-EVYLryarrALQ-DLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  92 EILDIknQELS-GTLTLYSRPSIAqCWLV-PALGDFTRRYPSISLTV----------LTGNDNvnlqragIDLAIYFDDA 159
Cdd:PRK11242   81 AIHDV--ADLSrGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTIremsqerieaLLADDE-------LDVGIAFAPV 150

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2058454114 160 PSAQLTHHFLMDEEILPVCS---PEYAQRHDLT 189
Cdd:PRK11242  151 HSPEIEAQPLFTETLALVVGrhhPLAARRKALT 183
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
41-154 6.03e-17

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 79.09  E-value: 6.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  41 LSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVywaLKSSLDTLNQ-----EILDIKNQELSGTLTLYSRPSIAQ 115
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEEL---RPFAQQTLLQwqqlrHTLDQQGPSLSGELSLFCSVTAAY 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2058454114 116 CWLVPALGDFTRRYPSISLTVLTGN--DNVNLQRAG-IDLAI 154
Cdd:PRK11716   80 SHLPPILDRFRAEHPLVEIKLTTGDaaDAVEKVQSGeADLAI 121
PRK09801 PRK09801
LysR family transcriptional regulator;
11-269 2.75e-16

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 77.77  E-value: 2.75e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  11 LLNGWQLSKLHTFEVAARHQ-SFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYwalKSSLDTL 89
Cdd:PRK09801    1 MLNSWPLAKDLQVLVEIVHSgSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY---EHALEIL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  90 NQ------EILDIKNQElSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDA-PSA 162
Cdd:PRK09801   78 TQyqrlvdDVTQIKTRP-EGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEiPDY 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 163 QLTHHFLMDEEILpVCSPEYAQRHDLTNTVINLSH--CTLLHDRqawsnDSGTDEWHSWAQHYAVNLPTSSGIGFDRSDL 240
Cdd:PRK09801  157 YIAHLLTKNKRIL-CAAPEYLQKYPQPQSLQELSRhdCLVTKER-----DMTHGIWELGNGQEKKSVKVSGHLSSNSGEI 230

                         250       260
                  ....*....|....*....|....*....
gi 2058454114 241 AVIAAMNHIGVAMGRKRLVQKRLASGELV 269
Cdd:PRK09801  231 VLQWALEGKGIMLRSEWDVLPFLESGKLV 259
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 29-270 4.87e-15

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 74.26  E-value: 4.87e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  29 HQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSL--DTLNQEILDIKNQELSGTLT 106
Cdd:PRK14997   16 EGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveAQAAQDAIAALQVEPRGIVK 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 107 LYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAP--SAQLTHHFLMDEEILPVCSPEYAQ 184
Cdd:PRK14997   96 LTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRVLADRGHRLFASPDLIA 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 185 RHDLTNTVINLSHCTLLhdrqawSNDSGTDEwHSWAQ----------HYAVNLPTSSGIGFDRsdlaviAAMNHIGVAMG 254
Cdd:PRK14997  176 RMGIPSAPAELSHWPGL------SLASGKHI-HRWELygpqgaraevHFTPRMITTDMLALRE------AAMAGVGLVQL 242

                         250
                  ....*....|....*.
gi 2058454114 255 RKRLVQKRLASGELVA 270
Cdd:PRK14997  243 PVLMVKEQLAAGELVA 258
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 15-99 1.84e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 72.28  E-value: 1.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  15 WQLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKrvyWALKSSLDTLNQeIL 94
Cdd:PRK11074    2 WSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE---WFVKEARSVIKK-MQ 77


                  ....*
gi 2058454114  95 DIKNQ 99
Cdd:PRK11074   78 ETRRQ 82
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
19-140 2.90e-14

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 71.93  E-value: 2.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  19 KLHTF----EVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVR-SHRKVELTHEGKRVYwalkSSLDTLNQEI 93
Cdd:PRK12684    2 NLHQLrfvrEAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIIL----ASVERILQEV 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2058454114  94 LDIK------NQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGN 140
Cdd:PRK12684   78 ENLKrvgkefAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGS 130
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
31-164 5.02e-13

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 68.25  E-value: 5.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  31 SFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQ--EILDIKNQELSGTLTLY 108
Cdd:PRK10632   18 SFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDvhEQLYAFNNTPIGTLRIG 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2058454114 109 SRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQL 164
Cdd:PRK10632   98 CSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSL 153
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
20-269 1.21e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 67.11  E-value: 1.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  20 LHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRShRKVELTHEGKRVYwALKSSLDTLNQEILdiknQ 99
Cdd:PRK03635    7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLL-RHARQVRLLEAELL----G 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 100 ELSGTLTLYSRPSIA------QCWLVPALGDFTRRYPsISLTVLTGNDNVNLQ--RAGIDL-AIYFDDAPSAQLTHHFLM 170
Cdd:PRK03635   81 ELPALDGTPLTLSIAvnadslATWFLPALAPVLARSG-VLLDLVVEDQDHTAEllRRGEVVgAVTTEPQPVQGCRVDPLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 171 DEEILPVCSPEYAQRH--------DLTNT-VINLSHCTLLHDRqaWSNDSGTDEWHSWAQHYavnLPTSSgiGFDRsdlA 241
Cdd:PRK03635  160 AMRYLAVASPAFAARYfpdgvtaeALAKApAVVFNRKDDLQDR--FLRQAFGLPPGSVPCHY---VPSSE--AFVR---A 229

                         250       260
                  ....*....|....*....|....*...
gi 2058454114 242 VIAAMnhiGVAMGRKRLVQKRLASGELV 269
Cdd:PRK03635  230 ALAGL---GWGMIPELQIEPELASGELV 254
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
16-201 2.69e-12

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 66.19  E-value: 2.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  16 QLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVywalkssLDTLNQEILD 95
Cdd:PRK15421    3 EVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEIL-------LQLANQVLPQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  96 IKNQELSGTLTLYSRPSIA-QC-----WLVPALGDFTRRYPSISLTVLTG---NDNVNLQRAGIDLAIYFDDAPSAQLTH 166
Cdd:PRK15421   76 ISQALQACNEPQQTRLRIAiEChsciqWLTPALENFHKNWPQVEMDFKSGvtfDPQPALQQGELDLVMTSDILPRSGLHY 155

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2058454114 167 HFLMDEEILPVCSPEYAQRHDLTNTVINLSHCTLL 201
Cdd:PRK15421  156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLL 190
rbcR CHL00180
LysR transcriptional regulator; Provisional
 17-136 2.99e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 2.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVywaLKSSLDTLN------ 90
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELL---LRYGNRILAlceetc 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2058454114  91 QEILDIKNQElSGTLTLYSRPSIAQcWLVPAL-GDFTRRYPSISLTV 136
Cdd:CHL00180   84 RALEDLKNLQ-RGTLIIGASQTTGT-YLMPRLiGLFRQRYPQINVQL 128
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-300 6.70e-12

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 8. 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: 176166  Cd Length: 197  Bit Score: 63.40  E-value: 6.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 118 LVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLSH 197
Cdd:cd08477    16 LTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDYLARHGTPTTPEDLAR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 198 ctllHDRQAWSNDSGTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMTV 277
Cdd:cd08477    96 ----HECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLVELLPDYLP 171

                         170       180
                  ....*....|....*....|...
gi 2058454114 278 KCHQHYYITTLPGRQWPKIEAFI 300
Cdd:cd08477   172 PPRPMHLLYPPDRRPTPKLRSFI 194
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-305 1.02e-10

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: 60.22  E-value: 1.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 111 PSIAQCWLVPALGDFTRRYPSISLtVLTGND-NVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRHDLT 189
Cdd:cd08472     9 GSLARLLLIPALPDFLARYPDIEL-DLGVSDrPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAYLARHGTP 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 190 NTVINLSHCTLLHDRqawSNDSG-TDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGEL 268
Cdd:cd08472    88 RHPEDLERHRAVGYF---SARTGrVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLASGRL 164

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2058454114 269 V-----APFGDMTVkchqhyYITTLPGRQW-PKIEAFITWLRE 305
Cdd:cd08472   165 VevlpdWRPPPLPV------SLLYPHRRHLsPRVRVFVDWVAE 201
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-281 1.52e-10

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: 59.49  E-value: 1.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 102 SGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAP---SAQLTHHFLMDEEILpVC 178
Cdd:cd08473     2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPledSSLVMRVLGQSRQRL-VA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 179 SPEYAQRHDLTNTVINLSHctllHDRQAWSNDSGTDEW---HSWAQHYAVNL-PTSSGigfdrSDLAVI--AAMNHIGVA 252
Cdd:cd08473    81 SPALLARLGRPRSPEDLAG----LPTLSLGDVDGRHSWrleGPDGESITVRHrPRLVT-----DDLLTLrqAALAGVGIA 151

                         170       180
                  ....*....|....*....|....*....
gi 2058454114 253 MGRKRLVQKRLASGELVAPFGDMTVKCHQ 281
Cdd:cd08473   152 LLPDHLCREALRAGRLVRVLPDWTPPRGI 180
PRK09791 PRK09791
LysR family transcriptional regulator;
16-198 1.64e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 60.93  E-value: 1.64e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  16 QLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLN--QEI 93
Cdd:PRK09791    6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRaaQED 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  94 LDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGN--DNVNLQRAG-IDLAI--YFDDAPSAQLTHHF 168
Cdd:PRK09791   86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQlvSMINELRQGeLDFTIntYYQGPYDHEFTFEK 165

                         170       180       190
                  ....*....|....*....|....*....|
gi 2058454114 169 LMDEEILPVCSPEYAQRHdlTNTVINLSHC 198
Cdd:PRK09791  166 LLEKQFAVFCRPGHPAIG--ARSLKQLLDY 193
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
20-79 2.89e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.98  E-value: 2.89e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  20 LHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRShRKVELTHEGKRVY 79
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLL 65
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 117-269 6.89e-10

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: 57.61  E-value: 6.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 117 WLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLS 196
Cdd:cd08479    15 HIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAYLERHGAPASPEDLA 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2058454114 197 HCTLLHDRQawsNDSGTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELV 269
Cdd:cd08479    95 RHDCLVIRE---NDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRSGRLV 164
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
20-75 7.69e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.05  E-value: 7.69e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2058454114  20 LHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEG 75
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAG 62
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-303 9.76e-10

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: 57.22  E-value: 9.76e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 104 TLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQ--RAG-IDLAIYFDDAPSAQLTHHFLMDEEILPVCSP 180
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEalLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 181 EYAQRHDLTNTVINLSHCTL-LHDRqawsnDSGTDEW-HSWAQHYAVNLPTSsgIGFDRSDLAVIAAMNHIGVAMGRKRL 258
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLiLFER-----GSGLRRLlDRAFAEAGFTPNIA--LEVDSLEAIKALVAAGLGIALLPESA 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2058454114 259 VQkRLASGELVA-PFGDMTVkcHQHYYITTLPGRQW-PKIEAFITWL 303
Cdd:cd05466   154 VE-ELADGGLVVlPLEDPPL--SRTIGLVWRKGRYLsPAARAFLELL 197
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 31-178 2.84e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.00  E-value: 2.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  31 SFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDIKN--QELSGTLTLY 108
Cdd:PRK11233   17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNvgQALSGQVSIG 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2058454114 109 SRP-SIAQCWLVPALGDFTRRYPSISL-------TVLtgNDNVNLQRagIDLAIYFDDAPSAQLTHHFLMDEEILPVC 178
Cdd:PRK11233   97 LAPgTAASSLTMPLLQAVRAEFPGIVLylhensgATL--NEKLMNGQ--LDMAVIYEHSPVAGLSSQPLLKEDLFLVG 170
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 16-135 7.05e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 56.15  E-value: 7.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  16 QLSKLHTFEVAARHqSFAL--AAEELSLSPSAVSHRINQLEEELGIQLFVRS-HRKVELTHEGKRVywaLKSSLDTLNqE 92
Cdd:PRK12682    2 NLQQLRFVREAVRR-NLNLteAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAV---LDVIERILR-E 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2058454114  93 ILDIK-------NQElSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLT 135
Cdd:PRK12682   77 VGNIKrigddfsNQD-SGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLS 125
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
20-134 1.62e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 54.64  E-value: 1.62e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  20 LHTF-EVA-ARHqsFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDIK 97
Cdd:PRK03601    6 LKTFlEVSrTRH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVA 83

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2058454114  98 NQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISL 134
Cdd:PRK03601   84 HTSQHNELSIGASASLWECMLTPWLGRLYQNQEALQF 120
PRK09986 PRK09986
LysR family transcriptional regulator;
1-102 3.24e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 53.96  E-value: 3.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114   1 MEPLREIRNRLLngwqlsklHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKrvyw 80
Cdd:PRK09986    1 MERLYRIDLKLL--------RYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGK---- 68

                          90       100
                  ....*....|....*....|..
gi 2058454114  81 ALKSSLDTLnqeiLDIKNQELS 102
Cdd:PRK09986   69 ILMEESRRL----LDNAEQSLA 86
PRK12680 PRK12680
LysR family transcriptional regulator;
34-149 1.00e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 52.70  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  34 LAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVE-LTHEGKRVYWALKSSLDTLNQEILDIKNQ--ELSGTLTLYSR 110
Cdd:PRK12680   21 LAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQrrESQGQLTLTTT 100

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2058454114 111 PSIAQCWLVPALGDFTRRYPSISltvltgndnVNLQRAG 149
Cdd:PRK12680  101 HTQARFVLPPAVAQIKQAYPQVS---------VHLQQAA 130
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 26-134 1.86e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.58  E-value: 1.86e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  26 AARhQSFAL--AAEELSLSPSAVSHRINQLEEELGIQLFVRS-HRKVELTHEGKRVywalkssLDTLNQEILDIKN---- 98
Cdd:PRK12683   12 AVR-QNFNLteVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKEL-------LQIVERMLLDAENlrrl 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2058454114  99 -----QELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISL 134
Cdd:PRK12683   84 aeqfaDRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHL 124
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-277 2.24e-07

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 6. 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: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 50.25  E-value: 2.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 120 PALGDFTRRYPSISLTvLTGND-NVNLQRAGIDLAIYFDD-APSAQLTHHFLmDEEILPVC-SPEYAQRHDLTNTVINL- 195
Cdd:cd08475    18 PLLLELARRHPELELE-LSFSDrFVDLIEEGIDLAVRIGElADSTGLVARRL-GTQRMVLCaSPAYLARHGTPRTLEDLa 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 196 SHCTLLHDRQawsndSGTDEWH-SWAQHYAVNLPTSSGIGFDRSDL---AVIAAMnhiGVAMGRKRLVQKRLASGELVAP 271
Cdd:cd08475    96 EHQCIAYGRG-----GQPLPWRlADEQGRLVRFRPAPRLQFDDGEAiadAALAGL---GIAQLPTWLVADHLQRGELVEV 167


                  ....*.
gi 2058454114 272 FGDMTV 277
Cdd:cd08475   168 LPELAP 173
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 17-140 4.84e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 50.46  E-value: 4.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYwalKSSLDTLNQ--EIL 94
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY---PRALALLEQavEIE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2058454114  95 DIKNQELsGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGN 140
Cdd:PRK10837   82 QLFREDN-GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGN 126
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-300 1.22e-06

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 5. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 48.23  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 102 SGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDapsaQLTHHflM-------DEEI 174
Cdd:cd08474     2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGE----SVEKD--MvavplgpPLRM 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 175 LPVCSPEYAQRH-------DLTNtvinlshctllHD--RQAWSNDSGTDEWH----SWAQHYAVNLPtssgIGFDRSDLA 241
Cdd:cd08474    76 AVVASPAYLARHgtpehprDLLN-----------HRciRYRFPTSGALYRWEfergGRELEVDVEGP----LILNDSDLM 140

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2058454114 242 VIAAMNHIGVAMGRKRLVQKRLASGELV--------APFGDmtvkcHQHYYittlPGRQWP-KIEAFI 300
Cdd:cd08474   141 LDAALDGLGIAYLFEDLVAEHLASGRLVrvledwspPFPGG-----YLYYP----SRRRVPpALRAFI 199
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 16-75 2.17e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 48.23  E-value: 2.17e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  16 QLSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEG 75
Cdd:PRK09906    2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAG 61
nhaR PRK11062
transcriptional activator NhaR; Provisional
 31-98 2.44e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 48.08  E-value: 2.44e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2058454114  31 SFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVY-WALKssLDTLNQEILDIKN 98
Cdd:PRK11062   20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFrYADK--MFTLSQEMLDIVN 86
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 113-301 2.60e-06

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 47.10  E-value: 2.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 113 IAQCWLVPALGDFTRRYPSISLTVLTGN--DNVNLQRAG-IDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEY--AQRHD 187
Cdd:cd08420    10 IGEYLLPRLLARFRKRYPEVRVSLTIGNteEIAERVLDGeIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHplAGRKE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 188 LtnTVINLSHCTLLhDRQAwsnDSGTDEW--HSWAQHyavnlptssgiGFDRSDLAVIAAMNHI-----------GVAMG 254
Cdd:cd08420    90 V--TAEELAAEPWI-LREP---GSGTREVfeRALAEA-----------GLDGLDLNIVMELGSTeaikeaveaglGISIL 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2058454114 255 RKRLVQKRLASGELVA-PFGDMTVKchQHYYITTLPGR-QWPKIEAFIT 301
Cdd:cd08420   153 SRLAVRKELELGRLVAlPVEGLRLT--RPFSLIYHKDKyLSPAAEAFLE 199
cbl PRK12679
HTH-type transcriptional regulator Cbl;
24-154 2.92e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 48.27  E-value: 2.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  24 EVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVR-SHRKVELTHEGKRVYWALKSSLDTLN--QEILDIKNQE 100
Cdd:PRK12679   11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERILNEASnvRRLADLFTND 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2058454114 101 LSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDN---VNLQRAGIDLAI 154
Cdd:PRK12679   91 TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQeiaTLLQNGEADIGI 147
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 118-303 4.29e-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: 4.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 118 LVPALGDFTRRYPSISLTvLTGNDN-VNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLS 196
Cdd:cd08478    18 LAPLIAKFRERYPDIELE-LVSNEGiIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHGTPQSIEDLA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 197 HctllHDRQAWSNDSGTDEW---HSWAQHYAVNLPTSSGIGFDRSDLaviaAMNHIGVAMGRKRLVQKRLASGELVAPFG 273
Cdd:cd08478    97 Q----HQLLGFTEPASLNTWpikDADGNLLKIQPTITASSGETLRQL----ALSGCGIACLSDFMTDKDIAEGRLIPLFA 168

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2058454114 274 DMTVKCHQH----YYITTLPGrqwPKIEAFITWL 303
Cdd:cd08478   169 EQTSDVRQPinavYYRNTALS---LRIRCFIDFL 199
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-270 1.72e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. 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: 176159  Cd Length: 197  Bit Score: 44.99  E-value: 1.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 118 LVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFddapsAQLTHHFLMDEEILP----VC-SPEYAQRHDLTNTV 192
Cdd:cd08470    16 IAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRL-----GRLTDSSLMARRLASrrhyVCaSPAYLERHGTPHSL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 193 INLSHctllHDRQAWSNDSgtdeWHSWAQHYAV------NLPTSSGigfdrsdLAVI-AAMNHIGVAMGRKRLVQKRLAS 265
Cdd:cd08470    91 ADLDR----HNCLLGTSDH----WRFQENGRERsvrvqgRWRCNSG-------VALLdAALKGMGLAQLPDYYVDEHLAA 155


                  ....*
gi 2058454114 266 GELVA 270
Cdd:cd08470   156 GRLVP 160
cysB PRK12681
HTH-type transcriptional regulator CysB;
24-134 1.93e-05

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 45.66  E-value: 1.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  24 EVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRS--HRKvELTHEGKRVYwalkssldTLNQEIL----DIK 97
Cdd:PRK12681   11 EVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSgkHLT-QVTPAGEEII--------RIAREILskveSIK 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2058454114  98 N--QELS----GTLTLYSRPSIAQCWLVPALGDFTRRYPSISL 134
Cdd:PRK12681   82 SvaGEHTwpdkGSLYIATTHTQARYALPPVIKGFIERYPRVSL 124
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 27-75 2.94e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 45.02  E-value: 2.94e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2058454114  27 ARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEG 75
Cdd:PRK11151   13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-189 8.69e-05

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 42.51  E-value: 8.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 111 PSIAQCWLVPALGDFTRRYPSISLTVL--TGNDNVNLQRAG-IDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEY--AQR 185
Cdd:cd08440     8 PSLAATLLPPVLAAFRRRHPGIRVRLRdvSAEQVIEAVRSGeVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHplARR 87


                  ....
gi 2058454114 186 HDLT 189
Cdd:cd08440    88 RSVT 91
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
20-305 1.05e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 43.12  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  20 LHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDIKNQ 99
Cdd:PRK10082   16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 100 E----------LSGTLTLYSRPSIAQcwLVPALgdFTRRYPSISLtvltgNDNVNLQRAGIDLAIYF---DDAPSAQLTH 166
Cdd:PRK10082   96 SdyaqrkikiaAAHSLSLGLLPSIIS--QMPPL--FTWAIEAIDV-----DEAVDKLREGQSDCIFSfhdEDLLEAPFDH 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 167 HFLMDEEILPVC-SPEYAQrhdltnTVINLS--HCTLLHdrqaWSNDS--GTDEWHSWAQHYAVNLPT---SSgigfdRS 238
Cdd:PRK10082  167 IRLFESQLFPVCaSDEHGE------ALFNLAqpHFPLLN----YSRNSymGRLINRTLTRHSELSFSTffvSS-----MS 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2058454114 239 DLAVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHyYITTLPGRQWPKIEAFITWLRE 305
Cdd:PRK10082  232 ELLKQVALDGCGIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQA-YAYRMNTRMNPVAERFWRELRE 297
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-300 1.08e-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 7. 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: 176165  Cd Length: 197  Bit Score: 42.62  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 118 LVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTH----HFLMdeeiLPVCSPEYAQRHDLTNTVI 193
Cdd:cd08476    14 LLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSrrlgSFRM----VLVASPDYLARHGTPETPA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 194 NLSHCTLLHDR-------QAWS--NDSGTDEwhswaqhyaVNLPTSsgIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLA 264
Cdd:cd08476    90 DLAEHACLRYRfpttgklEPWPlrGDGGDPE---------LRLPTA--LVCNNIEALIEFALQGLGIACLPDFSVREALA 158

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2058454114 265 SGELVAPFGDMTvkCHQ-HYYITTLPGRQW-PKIEAFI 300
Cdd:cd08476   159 DGRLVTVLDDYV--EERgQFRLLWPSSRHLsPKLRVFV 194
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-270 1.21e-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: 42.32  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 118 LVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRHDLTNTVINLSH 197
Cdd:cd08480    16 LLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSYLARHGTPLTPQDLAR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 198 ctllHDRQAWSNDSGTDEW------HSWAQHYAVNLPTSSGIGFDRsdLAVIAAmnhiGVAmgrkRL----VQKRLASGE 267
Cdd:cd08480    96 ----HNCLGFNFRRALPDWpfrdggRIVALPVSGNILVNDGEALRR--LALAGA----GLA----RLalfhVADDIAAGR 161


                  ...
gi 2058454114 268 LVA 270
Cdd:cd08480   162 LVP 164
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 17-75 2.00e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 42.32  E-value: 2.00e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2058454114  17 LSKLHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEG 75
Cdd:PRK15092   13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
PRK10341 PRK10341
transcriptional regulator TdcA;
20-76 2.18e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.16  E-value: 2.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2058454114  20 LHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGK 76
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQ 68
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-189 5.22e-04

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 40.28  E-value: 5.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 104 TLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQ--RAG-IDLAIY-FDDAPSAQLTHHFLMDEEILPVCS 179
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAavREGrLDLAFVgLPERRPPGLASRELAREPLVAVVA 80

                          90
                  ....*....|..
gi 2058454114 180 PEY--AQRHDLT 189
Cdd:cd08436    81 PDHplAGRRRVA 92
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-177 8.43e-04

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 39.89  E-value: 8.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 104 TLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGN--DNVNLQRAG-IDLAIYFDDAPSAQ-----LTHHFLMDEE-- 173
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEppESLDALRAGeLDLAVVFDYPVTPPpddpgLTRVPLLDDPld 80


                  ....*
gi 2058454114 174 -ILPV 177
Cdd:cd08423    81 lVLPA 85
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
36-85 1.43e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 36.42  E-value: 1.43e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2058454114   36 AEELSLSPSAVSHRINQLEEElGIqlfVRSHRkvelthEGKRVYWALKSS 85
Cdd:smart00418  17 AEILGLSQSTVSHHLKKLREA-GL---VESRR------EGKRVYYSLTDE 56
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 36-98 2.07e-03

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


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 36.51  E-value: 2.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2058454114  36 AEELSLSPSAVSHRINQLEEElGIqlfvrshrkVELTHEGKRVYWALkSSLDTLNQEILDIKN 98
Cdd:cd00090    27 AERLGLSQSTVSRHLKKLEEA-GL---------VESRREGRRVYYSL-TDAERLLALLESLLE 78
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 103-189 2.29e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 38.46  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 103 GTLTLYSRPSIAqCWLV-PALGDFTRRYPSISLTVL-TGNDNVN--LQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVC 178
Cdd:cd08425     1 GSLRLAMTPTFT-AYLIgPLIDRFHARYPGIALSLReMPQERIEaaLADDRLDLGIAFAPVRSPDIDAQPLFDERLALVV 79

                          90
                  ....*....|....
gi 2058454114 179 S---PEYAQRHDLT 189
Cdd:cd08425    80 GathPLAQRRTALT 93
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 35-138 4.79e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 4.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114  35 AAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSS---LDTLNQEILDIKNQElSGTLTLYSRP 111
Cdd:PRK11013   24 AARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAAESLREFR-QGQLSIACLP 102

                          90       100
                  ....*....|....*....|....*..
gi 2058454114 112 SIAQCWLVPALGDFTRRYPSISLTVLT 138
Cdd:PRK11013  103 VFSQSLLPGLCQPFLARYPDVSLNIVP 129
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 117-188 4.97e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 37.55  E-value: 4.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2058454114 117 WLVPALGDFTRRYPSISLTVLTG--NDNVN-LQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEyaqrHDL 188
Cdd:cd08441    14 WLMPVLDQFRERWPDVELDLSSGfhFDPLPaLLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPD----HPL 84
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 111-189 6.70e-03

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 37.25  E-value: 6.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2058454114 111 PSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQ--RAG-IDLAI--YFDDAPSAQLTHHFLMDEEILPVCSPEY--A 183
Cdd:cd08435     8 PAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEglRAGeLDLAIgrLADDEQPPDLASEELADEPLVVVARPGHplA 87


                  ....*.
gi 2058454114 184 QRHDLT 189
Cdd:cd08435    88 RRARLT 93
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
36-95 8.46e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.10  E-value: 8.46e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2058454114  36 AEELSLSPSAVSHRINQLEEElGiqlFVRSHR--------KVELTHEGKRVYWALKSSLDTLNQEILD 95
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLEEK-G---LVEREPdpedrravLVRLTEKGRALLEEARPALEALLAELLA 122
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 111-180 8.87e-03

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 36.80  E-value: 8.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2058454114 111 PSIAQCWLVPALGDFTRRYPSISLTVLTG-----NDNVNLQRagIDLAIYFDDAPSAQLTHHFLMDEEILPVCSP 180
Cdd:cd08433     8 PSAASVLAVPLLRAVRRRYPGIRLRIVEGlsghlLEWLLNGR--LDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
36-90 8.99e-03

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 37.18  E-value: 8.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2058454114  36 AEELSLSPSAVSHRINQLEEElgiQLFVRSHRKVELTHEGKRVYWALKSSLDTLN 90
Cdd:COG4742    36 AESLDVSRSTILRQLKELEER---GLIERDDGEYELTTLGRLVVEEMEPLLDTLE 87
 
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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