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Conserved domains on  [gi|612272112|gb|EZQ65617|]
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hypothetical protein AF54_00435 [Serratia marcescens BIDMC 81]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PenR_Burk_TF super family cl49228
beta-lactamase transcriptional regulator PenR; PenR, as the term is used in Burkholderia, is a ...
 1-286 1.96e-150

beta-lactamase transcriptional regulator PenR; PenR, as the term is used in Burkholderia, is a LysR-family transcriptional regulator of adjacent chromosomal class A beta-lactamase genes of the blaPEN family, which include blaPEN-A in B. multivorans, blaPEN-B in B. cenocepacia, etc.


The actual alignment was detected with superfamily member NF041130:

Pssm-ID: 469053 [Multi-domain]  Cd Length: 292  Bit Score: 422.88  E-value: 1.96e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIE 80
Cdd:NF041130   4 LRPHLPLNALRAFESSARHLNFTRAGLELSVTQAAVSQQVRSLEERLGCTLFTRLPRGLGLTDEGRALLPVLSDAFSRIE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  81 AVLQQFEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLF 160
Cdd:NF041130  84 TVLKQFDGGRFREVLTLGVVGTFAIGWLMPRLKRFGDTHPFVELRLRTNNNVVDLAAEGLDFAIRFGEGNWPATRNERLL 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 161 DAPLTVLCSPAVAARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFR 240
Cdd:NF041130 164 DAPLTALCAPEIARRLAQPADLANETLLRSYRTDEWLGWFDAAQLEPWTVNGPVFDSSRLMVEAAMQGAGVALAPACMFA 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 612272112 241 RELAAGALQRPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWICREA 286
Cdd:NF041130 244 RELQLGLLARPLDIDVHAGGYWLTSLKSKPLTPAMTLFRDWIVAEA 289
 
Name Accession Description Interval E-value
PenR_Burk_TF NF041130
beta-lactamase transcriptional regulator PenR; PenR, as the term is used in Burkholderia, is a ...
 1-286 1.96e-150

beta-lactamase transcriptional regulator PenR; PenR, as the term is used in Burkholderia, is a LysR-family transcriptional regulator of adjacent chromosomal class A beta-lactamase genes of the blaPEN family, which include blaPEN-A in B. multivorans, blaPEN-B in B. cenocepacia, etc.


Pssm-ID: 469053 [Multi-domain]  Cd Length: 292  Bit Score: 422.88  E-value: 1.96e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIE 80
Cdd:NF041130   4 LRPHLPLNALRAFESSARHLNFTRAGLELSVTQAAVSQQVRSLEERLGCTLFTRLPRGLGLTDEGRALLPVLSDAFSRIE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  81 AVLQQFEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLF 160
Cdd:NF041130  84 TVLKQFDGGRFREVLTLGVVGTFAIGWLMPRLKRFGDTHPFVELRLRTNNNVVDLAAEGLDFAIRFGEGNWPATRNERLL 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 161 DAPLTVLCSPAVAARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFR 240
Cdd:NF041130 164 DAPLTALCAPEIARRLAQPADLANETLLRSYRTDEWLGWFDAAQLEPWTVNGPVFDSSRLMVEAAMQGAGVALAPACMFA 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 612272112 241 RELAAGALQRPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWICREA 286
Cdd:NF041130 244 RELQLGLLARPLDIDVHAGGYWLTSLKSKPLTPAMTLFRDWIVAEA 289
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 94-282 8.35e-103

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: 298.13  E-value: 8.35e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 ARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQRPFA 253
Cdd:cd08484   81 RRLSEPADLANETLLRSYRADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQPFK 160

                        170       180
                 ....*....|....*....|....*....
gi 612272112 254 AEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08484  161 ITVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-291 6.04e-87

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 261.70  E-value: 6.04e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRLP-LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRI 79
Cdd:PRK11139   1 MSRRLPpLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  80 -EAVLQQFEGGHFHeVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIK 158
Cdd:PRK11139  81 aEATRKLRARSAKG-ALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 159 LFDAPLTVLCSPAVA---ARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRIN-GPVFDSSRLMVEGALQCDGVALA 234
Cdd:PRK11139 160 LLDEYLLPVCSPALLnggKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQqGPIFSHSSMALQAAIHGQGVALG 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 612272112 235 PVSMFRRELAAGALQRPF--AAEAALGAYWLTHLKSRDlTPAMKAFIGWICREAEEEQR 291
Cdd:PRK11139 240 NRVLAQPEIEAGRLVCPFdtVLPSPNAFYLVCPDSQAE-LPKVAAFRQWLLAEAAQEQE 297
chol_sulf_TF TIGR03418
putative choline sulfate-utilization transcription factor; Members of this protein family are ...
 5-285 8.60e-56

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


Pssm-ID: 188320 [Multi-domain]  Cd Length: 291  Bit Score: 181.86  E-value: 8.60e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112    5 LPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQ 84
Cdd:TIGR03418   1 LSLQWLRVFESAARLASFTAAARELGSTQPAVSQQIKRLEEELGVPLFERKHRGVELTEDGQRLFEAVRRGLDTIDAATA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   85 QFEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPL 164
Cdd:TIGR03418  81 ALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVSIVTSQDSHDGQRDDIDVAILFGDGRWPGGEAVRLFPEEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  165 TVLCSPAVAARLHTP---QDLQHELLM-----RTYRQDEWERWFTAAQVTPWRINGPV-FDSSRLMVEGALQCDGVALAP 235
Cdd:TIGR03418 161 TPVCSPALRAGLPDPlsaADLLRLPLLhleptQPARWFDWAGWFRALGLERPPAPGGLrFNNYTLVIQAAIAGQGVALGW 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 612272112  236 VSMFRRELAAGALQRPFAAEAALG-AYWLTHLKSRDLTPAMKAFIGWICRE 285
Cdd:TIGR03418 241 APLVDELLAAGQLVRLGDEPVVTErGYYLVRPPRKPRDAAVEAFRDWLLDE 291
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-288 2.36e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.27  E-value: 2.36e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   5 LPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQ 84
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  85 QFEGGHFHE--VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNN--LVN-LSADGMDFAIRFGEGLWPATRNIKL 159
Cdd:COG0583   81 ELRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrLVDaLLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 160 FDAPLTVLCSPAvaarlhtpqdlqHELLMRTyrqdewerwftaaqvtpwringPVFDSSRLMVEGALQCDGVALAPVSMF 239
Cdd:COG0583  161 GEERLVLVASPD------------HPLARRA----------------------PLVNSLEALLAAVAAGLGIALLPRFLA 206

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 612272112 240 RRELAAGAL-QRPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWICREAEE 288
Cdd:COG0583  207 ADELAAGRLvALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-282 1.17e-24

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: 98.13  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   95 LTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHN--NLVNLSADG-MDFAIRFGEGLWPATRNIKLFDAPLTVLCSPA 171
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  172 ---VAARLHTPQDLQHE-LLMRT---YRQDEWERWFTAAQVTPwrINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELA 244
Cdd:pfam03466  84 hplARGEPVSLEDLADEpLILLPpgsGLRDLLDRALRAAGLRP--RVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 612272112  245 AGALQ-RPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:pfam03466 162 DGRLVaLPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-69 8.78e-06

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 46.27  E-value: 8.78e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 612272112  22 FTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALL 69
Cdd:NF041036  18 FSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVL 65
 
Name Accession Description Interval E-value
PenR_Burk_TF NF041130
beta-lactamase transcriptional regulator PenR; PenR, as the term is used in Burkholderia, is a ...
 1-286 1.96e-150

beta-lactamase transcriptional regulator PenR; PenR, as the term is used in Burkholderia, is a LysR-family transcriptional regulator of adjacent chromosomal class A beta-lactamase genes of the blaPEN family, which include blaPEN-A in B. multivorans, blaPEN-B in B. cenocepacia, etc.


Pssm-ID: 469053 [Multi-domain]  Cd Length: 292  Bit Score: 422.88  E-value: 1.96e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIE 80
Cdd:NF041130   4 LRPHLPLNALRAFESSARHLNFTRAGLELSVTQAAVSQQVRSLEERLGCTLFTRLPRGLGLTDEGRALLPVLSDAFSRIE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  81 AVLQQFEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLF 160
Cdd:NF041130  84 TVLKQFDGGRFREVLTLGVVGTFAIGWLMPRLKRFGDTHPFVELRLRTNNNVVDLAAEGLDFAIRFGEGNWPATRNERLL 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 161 DAPLTVLCSPAVAARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFR 240
Cdd:NF041130 164 DAPLTALCAPEIARRLAQPADLANETLLRSYRTDEWLGWFDAAQLEPWTVNGPVFDSSRLMVEAAMQGAGVALAPACMFA 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 612272112 241 RELAAGALQRPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWICREA 286
Cdd:NF041130 244 RELQLGLLARPLDIDVHAGGYWLTSLKSKPLTPAMTLFRDWIVAEA 289
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 94-282 8.35e-103

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: 298.13  E-value: 8.35e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 ARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQRPFA 253
Cdd:cd08484   81 RRLSEPADLANETLLRSYRADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQPFK 160

                        170       180
                 ....*....|....*....|....*....
gi 612272112 254 AEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08484  161 ITVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 94-282 2.37e-98

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: 286.75  E-value: 2.37e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08487    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 ARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQRPFA 253
Cdd:cd08487   81 KRLSHPADLINETLLRSYRTDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQPFK 160

                        170       180
                 ....*....|....*....|....*....
gi 612272112 254 AEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08487  161 IEVETGSYWLTWLKSKPMTPAMELFRQWI 189
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-291 6.04e-87

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 261.70  E-value: 6.04e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRLP-LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRI 79
Cdd:PRK11139   1 MSRRLPpLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  80 -EAVLQQFEGGHFHeVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIK 158
Cdd:PRK11139  81 aEATRKLRARSAKG-ALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 159 LFDAPLTVLCSPAVA---ARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRIN-GPVFDSSRLMVEGALQCDGVALA 234
Cdd:PRK11139 160 LLDEYLLPVCSPALLnggKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQqGPIFSHSSMALQAAIHGQGVALG 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 612272112 235 PVSMFRRELAAGALQRPF--AAEAALGAYWLTHLKSRDlTPAMKAFIGWICREAEEEQR 291
Cdd:PRK11139 240 NRVLAQPEIEAGRLVCPFdtVLPSPNAFYLVCPDSQAE-LPKVAAFRQWLLAEAAQEQE 297
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 94-282 6.29e-79

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: 237.43  E-value: 6.29e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08488    1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 ARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTP--WRINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQRP 251
Cdd:cd08488   81 RQLREPADLARHTLLRSYRADEWPQWFEAAGVGHpcGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQP 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 612272112 252 FAAEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08488  161 FATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-282 7.85e-65

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: 201.65  E-value: 7.85e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 ARLH--TPQDLQHE-LLMRTYRQDEWERWFTAAQVT-PWRINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQ 249
Cdd:cd08432   81 AGLPllSPADLARHtLLHDATRPEAWQWWLWAAGVAdVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLV 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 612272112 250 RPFAAEAALG-AYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08432  161 RPFDLPLPSGgAYYLVYPPGRAESPAVAAFRDWL 194
chol_sulf_TF TIGR03418
putative choline sulfate-utilization transcription factor; Members of this protein family are ...
 5-285 8.60e-56

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


Pssm-ID: 188320 [Multi-domain]  Cd Length: 291  Bit Score: 181.86  E-value: 8.60e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112    5 LPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQ 84
Cdd:TIGR03418   1 LSLQWLRVFESAARLASFTAAARELGSTQPAVSQQIKRLEEELGVPLFERKHRGVELTEDGQRLFEAVRRGLDTIDAATA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   85 QFEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPL 164
Cdd:TIGR03418  81 ALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVSIVTSQDSHDGQRDDIDVAILFGDGRWPGGEAVRLFPEEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  165 TVLCSPAVAARLHTP---QDLQHELLM-----RTYRQDEWERWFTAAQVTPWRINGPV-FDSSRLMVEGALQCDGVALAP 235
Cdd:TIGR03418 161 TPVCSPALRAGLPDPlsaADLLRLPLLhleptQPARWFDWAGWFRALGLERPPAPGGLrFNNYTLVIQAAIAGQGVALGW 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 612272112  236 VSMFRRELAAGALQRPFAAEAALG-AYWLTHLKSRDLTPAMKAFIGWICRE 285
Cdd:TIGR03418 241 APLVDELLAAGQLVRLGDEPVVTErGYYLVRPPRKPRDAAVEAFRDWLLDE 291
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
1-290 3.30e-53

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 175.96  E-value: 3.30e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRL----PLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAF 76
Cdd:PRK10086   6 MRNRLlngwQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  77 DRIEAVLQQFEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRN 156
Cdd:PRK10086  86 DTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTH 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 157 IKLFDAPLTVLCSPAVAAR---LHTPQDLQHELLMRTyRQ--------DEWERWftaAQVTPWRINGP----VFDSSRLM 221
Cdd:PRK10086 166 HFLMDEEILPVCSPEYAERhalTGNPDNLRHCTLLHD-RQawsndsgtDEWHSW---AQHFGVNLLPPssgiGFDRSDLA 241

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 612272112 222 VEGALQCDGVALAPVSMFRRELAAGALQRPFAAEAAL--GAYWLTHLKSRdLTPAMKAFIGWICREAEEEQ 290
Cdd:PRK10086 242 VIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKchQHYYVTTLPGR-QWPKIEAFIDWLKEQVKTTS 311
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-288 2.36e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.27  E-value: 2.36e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   5 LPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQ 84
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  85 QFEGGHFHE--VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNN--LVN-LSADGMDFAIRFGEGLWPATRNIKL 159
Cdd:COG0583   81 ELRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrLVDaLLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 160 FDAPLTVLCSPAvaarlhtpqdlqHELLMRTyrqdewerwftaaqvtpwringPVFDSSRLMVEGALQCDGVALAPVSMF 239
Cdd:COG0583  161 GEERLVLVASPD------------HPLARRA----------------------PLVNSLEALLAAVAAGLGIALLPRFLA 206

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 612272112 240 RRELAAGAL-QRPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWICREAEE 288
Cdd:COG0583  207 ADELAAGRLvALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 94-282 1.05e-33

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: 121.63  E-value: 1.05e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 AR--LHTPQDLQH-ELLMRTYRQDEWERWFTAA---QVTPWRinGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGA 247
Cdd:cd08481   81 AGraLAAPADLAHlPLLQQTTRPEAWRDWFEEVgleVPTAYR--GMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGR 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 612272112 248 LQRPFAAE-AALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08481  159 LVVPFNLPlTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 95-282 6.04e-32

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: 117.06  E-value: 6.04e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  95 LTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAV-- 172
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLlg 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 173 AARLHTPQDLQHELLMRTYRQDEWERWFTAAQVTPWRINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQRPF 252
Cdd:cd08483   82 DRKVDSLADLAGLPWLQERGTNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTVLF 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 612272112 253 AAEAALGAYWLTHLKSRdLTPAMKAFIGWI 282
Cdd:cd08483  162 EEEEEGLGYHIVTRPGV-LRPAAKAFVRWL 190
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-282 1.17e-24

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: 98.13  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   95 LTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHN--NLVNLSADG-MDFAIRFGEGLWPATRNIKLFDAPLTVLCSPA 171
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  172 ---VAARLHTPQDLQHE-LLMRT---YRQDEWERWFTAAQVTPwrINGPVFDSSRLMVEGALQCDGVALAPVSMFRRELA 244
Cdd:pfam03466  84 hplARGEPVSLEDLADEpLILLPpgsGLRDLLDRALRAAGLRP--RVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 612272112  245 AGALQ-RPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:pfam03466 162 DGRLVaLPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-282 1.85e-23

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: 94.81  E-value: 1.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVA 173
Cdd:cd08422    2 RLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAYL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 AR---LHTPQDL-QHELLMRTY--RQDEWeRWFTAAQVTPWRINGP-VFDSSRLMVEGALQCDGVALAPVSMFRRELAAG 246
Cdd:cd08422   82 ARhgtPQTPEDLaRHRCLGYRLpgRPLRW-RFRRGGGEVEVRVRGRlVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 612272112 247 ALQRPFAA-EAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08422  161 RLVRVLPDwRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 95-282 4.65e-20

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: 85.53  E-value: 4.65e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  95 LTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIK-LFDAPLTVLCSPAVA 173
Cdd:cd08482    2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPAGMQVIeLFPERVGPVCSPSLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 174 ARLHTPQD-----LQHELLMRTYRQDEWERWFTAAQVTPWRIN-GPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGA 247
Cdd:cd08482   82 PTVPLRQApaaalLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGtGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGR 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 612272112 248 LQRPFAAEAAlGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08482  162 LVAPWGFIET-GSHYVLLRPARLRDSRAGALADWL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 2.22e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.04  E-value: 2.22e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112    7 LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-208 1.03e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 78.46  E-value: 1.03e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   7 LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLpvlsdafDRIEAVLQQF 86
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYL-------RYARRALQDL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  87 EGGH--FHEV-------LTVAVVGTFA---VGWLMprlAAFRAAHPFI--DLRVLTHNNL-VNLSADGMDFAIRFGEGLW 151
Cdd:PRK11242  76 EAGRraIHDVadlsrgsLRLAMTPTFTaylIGPLI---DAFHARYPGItlTIREMSQERIeALLADDELDVGIAFAPVHS 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612272112 152 PATRNIKLFDAPLTVLCSP--AVAARLH--TPQDLQHE---LLMRTY--RQDeWERWFTAAQVTPW 208
Cdd:PRK11242 153 PEIEAQPLFTETLALVVGRhhPLAARRKalTLDELADEplvLLSAEFatREQ-IDRYFRRHGVTPR 217
PRK09986 PRK09986
LysR family transcriptional regulator;
4-123 6.73e-16

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 76.30  E-value: 6.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   4 RLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVL 83
Cdd:PRK09986   6 RIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSL 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 612272112  84 QQFE--GGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFID 123
Cdd:PRK09986  86 ARVEqiGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVE 127
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-279 3.40e-15

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: 72.49  E-value: 3.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDA-PLTVLCSPAVAARlH----TPQDL 182
Cdd:cd08474   18 LAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPlRMAVVASPAYLAR-HgtpeHPRDL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 183 -QHELL-MRTYRQDEWERW-FT-AAQVTPWRINGP-VFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQR---PFAA 254
Cdd:cd08474   97 lNHRCIrYRFPTSGALYRWeFErGGRELEVDVEGPlILNDSDLMLDAALDGLGIAYLFEDLVAEHLASGRLVRvleDWSP 176

                        170       180
                 ....*....|....*....|....*
gi 612272112 255 EAAlgAYWLTHLKSRDLTPAMKAFI 279
Cdd:cd08474  177 PFP--GGYLYYPSRRRVPPALRAFI 199
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-148 2.32e-13

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 69.03  E-value: 2.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   7 LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIE-AVLQQ 85
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEkAKLRA 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612272112  86 FEGGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAHPfiDLRVlthnNLVNLSADGMDFAIRFGE 148
Cdd:PRK09906  83 RKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHP--DTLI----ELVSLITTQQEEKLRRGE 139
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-129 3.73e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 68.51  E-value: 3.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   5 LP--LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLpvlsDAFDRIEAV 82
Cdd:CHL00180   3 LPftLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLL----RYGNRILAL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 612272112  83 ----------LQQFEGGHfhevLTVA---VVGTFavgwLMPRLAA-FRAAHPFIDLRVLTH 129
Cdd:CHL00180  79 ceetcraledLKNLQRGT----LIIGasqTTGTY----LMPRLIGlFRQRYPQINVQLQVH 131
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-282 2.01e-12

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: 64.54  E-value: 2.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  95 LTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNN---LVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCS-- 169
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSselLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPpd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 170 -PAVAARLHTPQDLQHE-LLMRT---YRQDEWERWFTAAQVTPwrinGPVF--DSSRLMVEGALQCDGVALAPVSMFRRE 242
Cdd:cd05466   82 hPLAKRKSVTLADLADEpLILFErgsGLRRLLDRAFAEAGFTP----NIALevDSLEAIKALVAAGLGIALLPESAVEEL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 612272112 243 LAAGALQRPFAAEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-282 6.07e-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 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: 63.30  E-value: 6.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  95 LTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEglwpatrnikLFDAPL---------T 165
Cdd:cd08472    3 LRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGE----------LADSSLvarrlgelrM 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 166 VLC-SPAVAARL---HTPQDLQHELLM-----RTYRQDEWErWFTAAQVTPWRINGPV-FDSSRLMVEGALQCDGVALAP 235
Cdd:cd08472   73 VTCaSPAYLARHgtpRHPEDLERHRAVgyfsaRTGRVLPWE-FQRDGEEREVKLPSRVsVNDSEAYLAAALAGLGIIQVP 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 612272112 236 VSMFRRELAAGALqRPFAAEAALGAY--WLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08472  152 RFMVRPHLASGRL-VEVLPDWRPPPLpvSLLYPHRRHLSPRVRVFVDWV 199
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-124 2.32e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 63.09  E-value: 2.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   7 LNALRAFESSARH-LNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLF-RRLPRGLDLTEEGQALLPV----LSDAfDRIE 80
Cdd:PRK12682   3 LQQLRFVREAVRRnLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFiRHGKRLKGLTEPGKAVLDVieriLREV-GNIK 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 612272112  81 AVLQQF---EGGhfheVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDL 124
Cdd:PRK12682  82 RIGDDFsnqDSG----TLTIATTHTQARYVLPRVVAAFRKRYPKVNL 124
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 14-124 5.45e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 61.98  E-value: 5.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  14 ESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLF-RRLPRGLDLTEEGQALLPV----LSDAfDRIEAVLQQFEG 88
Cdd:PRK12683  11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFiRRGKRLTGLTEPGKELLQIvermLLDA-ENLRRLAEQFAD 89

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 612272112  89 GHFHEvLTVAVVGTFAVGWLMPRLAAFRAAHPFIDL 124
Cdd:PRK12683  90 RDSGH-LTVATTHTQARYALPKVVRQFKEVFPKVHL 124
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-285 1.49e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 60.77  E-value: 1.49e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   7 LNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQ-------ALLPVLSDAFDRI 79
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQtfyehckAMLVEAQAAQDAI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  80 EAVLQQFEGghfheVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFgeglwpATRNIKL 159
Cdd:PRK14997  84 AALQVEPRG-----IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRV------RPRPFED 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 160 FDAPLTVL--------CSPAVAARLHTPQ---DLQHellmrtyrqdeWERWFTAA--QVTPWRINGP------VFDSSRL 220
Cdd:PRK14997 153 SDLVMRVLadrghrlfASPDLIARMGIPSapaELSH-----------WPGLSLASgkHIHRWELYGPqgaraeVHFTPRM 221

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612272112 221 MV-------EGALQCDGVALAPVSMFRRELAAGALQRPFAA-EAALGAYWLTHLKSRDLTPAMKAFIGWICRE 285
Cdd:PRK14997 222 ITtdmlalrEAAMAGVGLVQLPVLMVKEQLAAGELVAVLEEwEPRREVIHAVFPSRRGLLPSVRALVDFLTEE 294
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-282 1.86e-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 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: 59.17  E-value: 1.86e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 102 TFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEglwpatrnikLFDAPL---------TVLC-SPA 171
Cdd:cd08477   10 TFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGE----------LADSSLvarplapyrMVLCaSPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 172 VAAR---LHTPQDL-QHELLMRTY--RQDEWeRWFTAAQVTPWRINGPV-FDSSRLMVEGALQCDGVALAPVSMFRRELA 244
Cdd:cd08477   80 YLARhgtPTTPEDLaRHECLGFSYwrARNRW-RLEGPGGEVKVPVSGRLtVNSGQALRVAALAGLGIVLQPEALLAEDLA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 612272112 245 AGALQRPFaAEAALGAYW--LTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08477  159 SGRLVELL-PDYLPPPRPmhLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-282 3.39e-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 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: 58.41  E-value: 3.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEglwpaTRNIKLFDAPL----TVLC-SPAVAARLHTPQD- 181
Cdd:cd08476   14 LLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGE-----LPDSRLMSRRLgsfrMVLVaSPDYLARHGTPETp 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 182 ---LQHELLMRtyrqdeweRWFTAAQVTPWRINGP------------VFDSSRLMVEGALQCDGVALAPVSMFRRELAAG 246
Cdd:cd08476   89 adlAEHACLRY--------RFPTTGKLEPWPLRGDggdpelrlptalVCNNIEALIEFALQGLGIACLPDFSVREALADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 612272112 247 ALQRPFAAE-AALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08476  161 RLVTVLDDYvEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-254 3.76e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.65  E-value: 3.76e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   7 LNALRAFESSArhlNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQQF 86
Cdd:PRK15421   7 LKTLQALRNCG---SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAC 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  87 EGGHfHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRV---LTHNNLVNLSADGMDFAI------RFGEGLWPatrni 157
Cdd:PRK15421  84 NEPQ-QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFksgVTFDPQPALQQGELDLVMtsdilpRSGLHYSP----- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 158 kLFDAPLTVLCSP--AVAARLH-TPQDLQHELLM----RTYRQDEWERWFTAAQVTPwriNGPVFDSSRLMVEGALQCDG 230
Cdd:PRK15421 158 -MFDYEVRLVLAPdhPLAAKTRiTPEDLASETLLiypvQRSRLDVWRHFLQPAGVSP---SLKSVDNTLLLIQMVAARMG 233

                        250       260       270
                 ....*....|....*....|....*....|....
gi 612272112 231 VALAP---VSMFRRE-------LAAGALQRPFAA 254
Cdd:PRK15421 234 IAALPhwvVESFERQglvvtktLGEGLWSRLYAA 267
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-119 1.28e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.06  E-value: 1.28e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  10 LRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRlPRGLDLTEEGQALLPVLsDAFDRIEAVLQQ--FE 87
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHL-RQVALLEADLLStlPA 84

                         90       100       110
                 ....*....|....*....|....*....|..
gi 612272112  88 GGHFHEVLTVAVVGTFAVGWLMPRLAAFRAAH 119
Cdd:PRK13348  85 ERGSPPTLAIAVNADSLATWFLPALAAVLAGE 116
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-94 1.96e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 57.51  E-value: 1.96e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   4 RLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAV- 82
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMp 80

                         90
                 ....*....|....
gi 612272112  83 --LQQFEGGHFHEV 94
Cdd:PRK10094  81 seLQQVNDGVERQV 94
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
14-168 3.05e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 53.83  E-value: 3.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  14 ESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRL-PRGLDLTEEGQALLP----VLSDAfDRIEAVLQQF-- 86
Cdd:PRK12684  11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILAsverILQEV-ENLKRVGKEFaa 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  87 -EGGHFhevlTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHN-----NLVnlSADGMDFAIrfgeglwpATRNIKLF 160
Cdd:PRK12684  90 qDQGNL----TIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSptqiaEMV--LHGQADLAI--------ATEAIADY 155


                 ....*...
gi 612272112 161 DAPLTVLC 168
Cdd:PRK12684 156 KELVSLPC 163
cbl PRK12679
HTH-type transcriptional regulator Cbl;
14-124 3.40e-08

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 53.66  E-value: 3.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  14 ESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLF-RRLPRGLDLTEEGQALLP----VLSDAFD--RIEAVLQQF 86
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLViaerILNEASNvrRLADLFTND 90

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 612272112  87 EGGhfheVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDL 124
Cdd:PRK12679  91 TSG----VLTIATTHTQARYSLPEVIKAFRELFPEVRL 124
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 108-282 7.91e-08

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: 51.57  E-value: 7.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEgLWPATRNIK-LFDAPLTVLCSPAVAARLHTPQ---DLQ 183
Cdd:cd08478   18 LAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGE-LTDSTLHARpLGKSRLRILASPDYLARHGTPQsieDLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 184 HELLMRTYRQDEWERW-FTAAQVTPWRIN-GPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQRPFAAEAALG-- 259
Cdd:cd08478   97 QHQLLGFTEPASLNTWpIKDADGNLLKIQpTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFAEQTSDVrq 176

                        170       180
                 ....*....|....*....|...
gi 612272112 260 AYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08478  177 PINAVYYRNTALSLRIRCFIDFL 199
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
21-169 1.95e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 51.59  E-value: 1.95e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  21 NFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQQFEGG--HFHEVLTVA 98
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGsdYAQRKIKIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  99 VVGTFAVGWL------MPRLaaFRAAHPFIDLrvlthNNLVNLSADGM-DFAIRF-GEGLWPAT-RNIKLFDAPLTVLCS 169
Cdd:PRK10082 107 AAHSLSLGLLpsiisqMPPL--FTWAIEAIDV-----DEAVDKLREGQsDCIFSFhDEDLLEAPfDHIRLFESQLFPVCA 179
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-282 5.14e-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: 49.09  E-value: 5.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLC-SPAVAARLHTPQDL---- 182
Cdd:cd08475   16 VAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTGLVARRLGTQRMVLCaSPAYLARHGTPRTLedla 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 183 QHELLMrtYRQdewerwftAAQVTPWRINGP-------------VFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQ 249
Cdd:cd08475   96 EHQCIA--YGR--------GGQPLPWRLADEqgrlvrfrpaprlQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELV 165

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 612272112 250 R----PFAAEAALGAYWlthLKSRDLTPAMKAFIGWI 282
Cdd:cd08475  166 EvlpeLAPEGLPIHAVW---PRTRHLPPKVRAAVDAL 199
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
15-70 6.16e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.63  E-value: 6.16e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 612272112  15 SSARHlnFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLP 70
Cdd:PRK03601  13 SRTRH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLP 66
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 17-66 9.28e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.17  E-value: 9.28e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 612272112  17 ARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQ 66
Cdd:PRK11074  14 ARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PRK09791 PRK09791
LysR family transcriptional regulator;
1-127 1.48e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 48.60  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   1 MRNRLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIE 80
Cdd:PRK09791   1 MAFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 612272112  81 AV---LQQfEGGHFHEVLTVAVVGTFAVGwLMPR-LAAFRAAHPFIDLRVL 127
Cdd:PRK09791  81 AAqedIRQ-RQGQLAGQINIGMGASIARS-LMPAvISRFHQQHPQVKVRIM 129
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-126 2.00e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 48.23  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   4 RLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRlPRGLDLTEEGQALLPvLSDAFDRIEAVL 83
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLR-HARQVRLLEAEL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 612272112  84 QQ--FEGGHFHEVLTVAV----VGTfavgWLMPRLAAFRAAHPF-IDLRV 126
Cdd:PRK03635  79 LGelPALDGTPLTLSIAVnadsLAT----WFLPALAPVLARSGVlLDLVV 124
cysB PRK12681
HTH-type transcriptional regulator CysB;
7-161 4.24e-06

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 47.59  E-value: 4.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   7 LNALRAFESSARH-LNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGL-DLTEEGQALL----PVLSDAfDRIE 80
Cdd:PRK12681   3 LQQLRYIVEVVNHnLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIriarEILSKV-ESIK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  81 AVLQQFEGGHfHEVLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVL--THNNLVNLSADG-MDFAIrfgeglwpATRNI 157
Cdd:PRK12681  82 SVAGEHTWPD-KGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHqgSPTQIAEAAAKGnADFAI--------ATEAL 152


                 ....
gi 612272112 158 KLFD 161
Cdd:PRK12681 153 HLYD 156
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-124 5.06e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 46.99  E-value: 5.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112   4 RLPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLP---VLSDAFDRIE 80
Cdd:PRK10837   2 HITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPralALLEQAVEIE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 612272112  81 AVLQQFEGGhfhevLTVAVVGTFAVGWLMPRLAAFRAAHPFIDL 124
Cdd:PRK10837  82 QLFREDNGA-----LRIYASSTIGNYILPAMIARYRRDYPQLPL 120
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-69 8.78e-06

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 46.27  E-value: 8.78e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 612272112  22 FTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALL 69
Cdd:NF041036  18 FSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVL 65
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-250 1.66e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 44.85  E-value: 1.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 102 TFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNI--KLFDAPLTVLCSPAVAARL--- 176
Cdd:cd08473   12 ALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEDSSLVmrVLGQSRQRLVASPALLARLgrp 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 612272112 177 HTPQDLQHELLMRTYRQDEWERW-FTAAQVTPWRIN-GPVFDSSRLMV--EGALQCDGVALAPVSMFRRELAAGALQR 250
Cdd:cd08473   92 RSPEDLAGLPTLSLGDVDGRHSWrLEGPDGESITVRhRPRLVTDDLLTlrQAALAGVGIALLPDHLCREALRAGRLVR 169
PRK09801 PRK09801
LysR family transcriptional regulator;
21-262 1.71e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 45.41  E-value: 1.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  21 NFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQ-------ALLPVLSDAFDRIEAVLQQFEGghfhe 93
Cdd:PRK09801  22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrcyehalEILTQYQRLVDDVTQIKTRPEG----- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLwPATRNIKLFDAPLTVLC-SPAV 172
Cdd:PRK09801  97 MIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEI-PDYYIAHLLTKNKRILCaAPEY 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 173 AARLHTPQDLQ----HELLM---RTYRQDEWERWfTAAQVTPWRINGPV-FDSSRLMVEGALQCDGValapvsMFRRE-- 242
Cdd:PRK09801 176 LQKYPQPQSLQelsrHDCLVtkeRDMTHGIWELG-NGQEKKSVKVSGHLsSNSGEIVLQWALEGKGI------MLRSEwd 248

                        250       260
                 ....*....|....*....|....
gi 612272112 243 ----LAAGALQRPFAAEAALGAYW 262
Cdd:PRK09801 249 vlpfLESGKLVQVLPEYAQSANIW 272
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-250 2.53e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 44.12  E-value: 2.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  99 VVGTFAVG--WLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGlwPATRNI--KLfdAPLT-VLC-SPAV 172
Cdd:cd08479    5 VNASFGFGrrHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDL--PDSSLIarKL--APNRrILCaSPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 173 AARLHTPQDL----QHELLMrtYRQDE-----WeRWFTAAQVTPWRINGP-VFDSSRLMVEGALQCDGVALAPVSMFRRE 242
Cdd:cd08479   81 LERHGAPASPedlaRHDCLV--IRENDedfglW-RLRNGDGEATVRVRGAlSSNDGEVVLQWALDGHGIILRSEWDVAPY 157


                 ....*...
gi 612272112 243 LAAGALQR 250
Cdd:cd08479  158 LRSGRLVR 165
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 95-282 3.04e-05

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 44.03  E-value: 3.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  95 LTVAVVGTfaVGWLMPR-LAAFRAAHPFID--LRVLTHNNLVNLSADG-MDFAIrFG---EGLwpATRNIKLFDAPLTVL 167
Cdd:cd08419    2 LRLAVVST--AKYFAPRlLGAFCRRHPGVEvsLRVGNREQVLERLADNeDDLAI-MGrppEDL--DLVAEPFLDNPLVVI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 168 CSPA---VAARLHTPQDLQHE-LLMR-----TyRQDeWERWFTAAQVTPwringpvfdSSRL----------MVEGALqc 228
Cdd:cd08419   77 APPDhplAGQKRIPLERLAREpFLLRepgsgT-RLA-MERFFAEHGVTL---------RVRMelgsneaikqAVMAGL-- 143

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 612272112 229 dGVALAPVSMFRRELAAGALQRPFAAEAALGAYW-LTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08419  144 -GLSVLSLHTLALELATGRLAVLDVEGFPIRRQWyVVHRKGKRLSPAAQAFLDFL 197
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-69 3.92e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 44.25  E-value: 3.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 612272112   5 LPLNALRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALL 69
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLL 75
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 23-147 6.25e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.90  E-value: 6.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  23 TRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEG-------QALLPVLSDAFDRIEAVLQQFEGghfhevl 95
Cdd:PRK11233  19 TQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGkilythaRAILRQCEQAQLAVHNVGQALSG------- 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  96 TVAV---VGTFAVGWLMPRLAAFRAAHPfiDLRVLTHNN----LVNLSADG-MDFAIRFG 147
Cdd:PRK11233  92 QVSIglaPGTAASSLTMPLLQAVRAEFP--GIVLYLHENsgatLNEKLMNGqLDMAVIYE 149
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-248 1.13e-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: 1.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 103 FAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVAARL---HTP 179
Cdd:cd08480   11 FGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSYLARHgtpLTP 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 180 QDL-QHELLMRTYRQdewerwftAAQVTPWRINGPVFDssrLMVEGALQCD-----------GVALAPVSMF--RRELAA 245
Cdd:cd08480   91 QDLaRHNCLGFNFRR--------ALPDWPFRDGGRIVA---LPVSGNILVNdgealrrlalaGAGLARLALFhvADDIAA 159


                 ...
gi 612272112 246 GAL 248
Cdd:cd08480  160 GRL 162
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-281 1.31e-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 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176160  Cd Length: 201  Bit Score: 42.13  E-value: 1.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEglwpatrnikLFDAPLT---------VLC-SPAVAAR-- 175
Cdd:cd08471   16 VLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGH----------LPDSSLVatrvgsvrrVVCaSPAYLARhg 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 176 -LHTPQDL-QHELLMrtyrqdewerwFTAAQVTP-WRINGPVFD-----SSRLMV---EGALQ--CDGVALAPVSMF--R 240
Cdd:cd08471   86 tPKHPDDLaDHDCIA-----------FTGLSPAPeWRFREGGKErsvrvRPRLTVntvEAAIAaaLAGLGLTRVLSYqvA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 612272112 241 RELAAGALQRPFAA--EAALGAYwLTHLKSRDLTPAMKAFIGW 281
Cdd:cd08471  155 EELAAGRLQRVLEDfePPPLPVH-LVHPEGRLAPAKVRAFVDF 196
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 108-279 1.98e-04

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: 41.71  E-value: 1.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPR-LAAFRAAHPFIDLRVLTHNN--LVNLSADG-MDFAIRFGEGLWPATRNIKLFDAPLTVLCSPA---VAARLHTPQ 180
Cdd:cd08420   14 LLPRlLARFRKRYPEVRVSLTIGNTeeIAERVLDGeIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDhplAGRKEVTAE 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 181 DLQHE-LLMR-----TyRQdEWERWFTAAQVTPWRIN-GPVFDSSRLMVEGALQCDGVALAPVSMFRRELAAGALQ---- 249
Cdd:cd08420   94 ELAAEpWILRepgsgT-RE-VFERALAEAGLDGLDLNiVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLValpv 171

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 612272112 250 ------RPFaaeaalgaYWLTHlKSRDLTPAMKAFI 279
Cdd:cd08420  172 eglrltRPF--------SLIYH-KDKYLSPAAEAFL 198
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-128 2.45e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 41.73  E-value: 2.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  31 VTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALLPVLSDAFDRIEAVLQQFEGGH---------FHEVltvavvg 101
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGpslsgelslFCSV------- 75

                         90       100
                 ....*....|....*....|....*..
gi 612272112 102 TFAVGWLMPRLAAFRAAHPFIDLRVLT 128
Cdd:PRK11716  76 TAAYSHLPPILDRFRAEHPLVEIKLTT 102
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-248 3.54e-04

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: 40.76  E-value: 3.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 108 LMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFGEGLWPATRNIKLFDAPLTVLCSPAVAARLHTPQDL----Q 183
Cdd:cd08470   16 IAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAYLERHGTPHSLadldR 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612272112 184 HELLMRT-----YRQDEWERwftaaQVTP---WRINgpvfdSSRLMVEGALQCDGVALAPVSMFRRELAAGAL 248
Cdd:cd08470   96 HNCLLGTsdhwrFQENGRER-----SVRVqgrWRCN-----SGVALLDAALKGMGLAQLPDYYVDEHLAAGRL 158
PRK10341 PRK10341
transcriptional regulator TdcA;
10-69 4.35e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.39  E-value: 4.35e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  10 LRAFESSARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALL 69
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLL 71
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-147 6.29e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 40.51  E-value: 6.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  22 FTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQALlpvlsdaFDRIEAVLQQFEggHFHE-------- 93
Cdd:PRK10632  19 FTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIY-------YQGCRRMLHEVQ--DVHEqlyafnnt 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 612272112  94 ---VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNNLVNLSADGMDFAIRFG 147
Cdd:PRK10632  90 pigTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVG 146
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 17-69 6.82e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 40.40  E-value: 6.82e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  17 ARHLNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPR-------GLDLTEEGQALL 69
Cdd:PRK11151  13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRkvlftqaGLLLVDQARTVL 72
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-282 9.24e-04

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: 39.56  E-value: 9.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHPFIDLRVLTHNN---LVNLSADGMDFAI-RFGEGLW-PATRNIKLFDAPLtvlc 168
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSdelLEGLRAGELDLAIgRLADDEQpPDLASEELADEPL---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 169 spAVAARLHTPQDLQHELLMRTYRQDEW-------------ERWFTAAQVTPWR--INGPVFDSSRLMVEGAlqcDGVAL 233
Cdd:cd08435   77 --VVVARPGHPLARRARLTLADLADYPWvlpppgtplrqrlEQLFAAAGLPLPRnvVETASISALLALLARS---DMLAV 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 612272112 234 APVSMFRRELAAGALQR-PFAAEAALGAYWLTHLKSRDLTPAMKAFIGWI 282
Cdd:cd08435  152 LPRSVAEDELRAGVLRElPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PRK12680 PRK12680
LysR family transcriptional regulator;
20-120 1.03e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 39.99  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  20 LNFTRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLD-LTEEGQALL----PVLSDAFD-RIEAVLQQFEGghfHE 93
Cdd:PRK12680  17 LNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIerarAVLSEANNiRTYAANQRRES---QG 93

                         90       100
                 ....*....|....*....|....*..
gi 612272112  94 VLTVAVVGTFAVGWLMPRLAAFRAAHP 120
Cdd:PRK12680  94 QLTLTTTHTQARFVLPPAVAQIKQAYP 120
nhaR PRK11062
transcriptional activator NhaR; Provisional
 19-66 1.94e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.22  E-value: 1.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612272112  19 HLNF---------------TRAGLELRVTQAAVSQQVRMLEEQLGIQLFRRLPRGLDLTEEGQ 66
Cdd:PRK11062   3 HINYnhlyyfwmvckegsvVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 95-279 3.48e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 37.93  E-value: 3.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112  95 LTVAVVGTFAVGwLMPR-LAAFRAAHPFIDLRVLTHN--NLVNLSADG-MDFAIRFGEGLWPATRNIKLFDAPLTVLCSP 170
Cdd:cd08415    2 LRIAALPALALS-LLPRaIARFRARHPDVRISLHTLSssTVVEAVLSGqADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 171 ----AVAARLhTPQDLQHELLMRTYRQDEW----ERWFTAAQVTP-WRINGPVFDSSRLMVEGALqcdGVAL---APVSM 238
Cdd:cd08415   81 ghplARKDVV-TPADLAGEPLISLGRGDPLrqrvDAAFERAGVEPrIVIETQLSHTACALVAAGL---GVAIvdpLTAAG 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 612272112 239 FRrelAAGALQRPFAAEAALGAYwLTHLKSRDLTPAMKAFI 279
Cdd:cd08415  157 YA---GAGLVVRPFRPAIPFEFA-LVRPAGRPLSRLAQAFI 193
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 102-280 8.18e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 36.82  E-value: 8.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 102 TFAVGWLMPRLAAFRAAHPFIDLRVLTHNN--LVNLSADG-MDFAIRFGEGLWPATRNIKLFDAPLtVLCSPAVAARLHT 178
Cdd:cd08442    9 TTAAVRLPPLLAAYHARYPKVDLSLSTGTTgaLIQAVLEGrLDGAFVAGPVEHPRLEQEPVFQEEL-VLVSPKGHPPVSR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612272112 179 PQDLQHE--LLMRT---YRQdEWERWFTAAQVTPwrinGPVFDSSRLmvEGALQC----DGVALAPVSMFRRELAAGALQ 249
Cdd:cd08442   88 AEDLAGStlLAFRAgcsYRR-RLEDWLAEEGVSP----GKIMEFGSY--HAILGCvaagMGIALLPRSVLDSLQGRGSVS 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 612272112 250 R-PFAAEAALGAYWLTHlkSRD-LTPAMKAFIG 280
Cdd:cd08442  161 IhPLPEPFADVTTWLVW--RKDsFTAALQAFLD 191
 
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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