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Conserved domains on  [gi|1502692554|ref|WP_122316484|]
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LysR substrate-binding domain-containing protein [Pseudomonas cichorii]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 4-294 5.89e-84

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 254.38  E-value: 5.89e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   4 RRLtPSMSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIR 83
Cdd:PRK11139    3 RRL-PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  84 SATLQTIAhKSEGGTLHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMNAVICAGTGHWPGYVAH 163
Cdd:PRK11139   82 EATRKLRA-RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPD--IDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 164 PLIAEKLVLIASPSALPGHQAM-TPAEVAQHSLLGVVSRpNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIA 242
Cdd:PRK11139  159 KLLDEYLLPVCSPALLNGGKPLkTPEDLARHTLLHDDSR-EDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVA 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1502692554 243 LVPRILVQDEISSGELVTLF-EPMDSGRNYYLVYATRFQNLPSLCVFRDWLLS 294
Cdd:PRK11139  238 LGNRVLAQPEIEAGRLVCPFdTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLA 290
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 4-294 5.89e-84

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 254.38  E-value: 5.89e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   4 RRLtPSMSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIR 83
Cdd:PRK11139    3 RRL-PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  84 SATLQTIAhKSEGGTLHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMNAVICAGTGHWPGYVAH 163
Cdd:PRK11139   82 EATRKLRA-RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPD--IDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 164 PLIAEKLVLIASPSALPGHQAM-TPAEVAQHSLLGVVSRpNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIA 242
Cdd:PRK11139  159 KLLDEYLLPVCSPALLNGGKPLkTPEDLARHTLLHDDSR-EDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVA 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1502692554 243 LVPRILVQDEISSGELVTLF-EPMDSGRNYYLVYATRFQNLPSLCVFRDWLLS 294
Cdd:PRK11139  238 LGNRVLAQPEIEAGRLVCPFdTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLA 290
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 98-292 1.41e-59

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: 188.66  E-value: 1.41e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPS 177
Cdd:cd08481     1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDF--SQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 178 ALPGHQAMTPAEVAQHSLLGVVSRPNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSGE 257
Cdd:cd08481    79 LLAGRALAAPADLAHLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGR 158

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1502692554 258 LVTLFE-PMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08481   159 LVVPFNlPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-294 3.09e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.97  E-value: 3.09e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIRSATLQTIA 91
Cdd:COG0583     5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  92 HKSE-GGTLHLAVLPTFGSKWLLPRMHDFYARHPD---HVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIA 167
Cdd:COG0583    85 LRGGpRGTLRIGAPPSLARYLLPPLLARFRARHPGvrlELREGNSDRLVDAL--LEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 168 EKLVLIASPsalpghqamtpaevaqhsllgvvsrpnawsdwfdrnqlDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRI 247
Cdd:COG0583   163 ERLVLVASP--------------------------------------DHPLARRAPLVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1502692554 248 LVQDEISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRDWLLS 294
Cdd:COG0583   205 LAADELAAGRLVALpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-293 9.25e-28

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: 106.60  E-value: 9.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLTP-ATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIAS 175
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLlLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 176 PS-ALPGHQAMTPAEVAQHSLLgVVSRPNAWSDWFDRNQLDHHI-MRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEI 253
Cdd:pfam03466  82 PDhPLARGEPVSLEDLADEPLI-LLPPGSGLRDLLDRALRAAGLrPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1502692554 254 SSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRDWLL 293
Cdd:pfam03466 161 ADGRLVALpLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-290 6.34e-22

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 93.07  E-value: 6.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   1 MNPRRLTpsmslliAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAG-ALYQH------ 73
Cdd:NF040786    1 MNLKQLE-------AFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGkLLYEYakemld 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  74 ---ELAAALGRIRsatlqtiahKSEGGTLHLAVlPTFGSKWLLPRM-HDFYARHPDHVVHV---HSRIVHADLtpatSEM 146
Cdd:NF040786   74 lweKLEEEFDRYG---------KESKGVLRIGA-STIPGQYLLPELlKKFKEKYPNVRFKLmisDSIKVIELL----LEG 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 147 NAVIcAGTGHWP---GYVAHPLIAEKLVLIAsPSALPGHQAMTPAEVAQHsllgVVSRPNAW----SDwfDRNQLDHHIM 219
Cdd:NF040786  140 EVDI-GFTGTKLekkRLVYTPFYKDRLVLIT-PNGTEKYRMLKEEISISE----LQKEPFIMreegSG--TRKEAEKALK 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 220 RPG---------PSFELTAHLIQAVAAGIGIALVPRILVQDEISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFR 289
Cdd:NF040786  212 SLGisledlnvvASLGSTEAIKQSVEAGLGISVISELAAEKEVERGRVLIFpIPGLPKNRDFYLVYNKNRQLSPTAEAFL 291


                  .
gi 1502692554 290 D 290
Cdd:NF040786  292 Q 292
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 12-261 2.65e-15

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 74.57  E-value: 2.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRdGRRIELTTAG----------ALYQHELAAALGR 81
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGqrllrharqvRLLEAELLAELPG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  82 IRSATLQTIAhkseggtlhLAV----LPTfgskWLLPRMHDFYARHP-------DHVVHVHSRIVHADLTPA-TSEMNAV 149
Cdd:TIGR03298  84 LAPGAPTRLT---------IAVnadsLAT----WFLPALAPVLAREGvlldlvvEDQDHTAELLRSGEVLGAvTTEAKPV 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 150 icagtghwPGYVAHPLIAEKLVLIASPSAlpgHQAMTPAEVAQHSLLG----VVSRPNAWSDWFDRNQLDHHIMRPG--- 222
Cdd:TIGR03298 151 --------PGCRVVPLGAMRYLAVASPAF---AARYFPDGVTAAALARapviVFNRKDDLQDRFLRRLFGLPVSPPRhyv 219

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1502692554 223 PSfelTAHLIQAVAAGIGIALVPRILVQDEISSGELVTL 261
Cdd:TIGR03298 220 PS---SEGFVDAARAGLGWGMVPELQAEPHLAAGRLVEL 255
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 19-259 2.92e-13

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: 68.61  E-value: 2.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  19 AARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGrIRSATLQTIAHKSEGGT 98
Cdd:NF041036   12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILD-IEDSLMDELKSFKGRQR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMN-----AVI--CAGTGHWPgYVAHPLIAEKLV 171
Cdd:NF041036   91 LSICCTPTFGMAHLPGVLNRFMLRNAD--VVDLKFLFHSPAQALEGIQNkefdlAIIehCADLDLGR-FHTYPLPQDELV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 172 LIASPSALPGHQAMTPAEVAQHSLlgvVSRPNAWSdwfDRNQLDHHIMRPGPSFE------------LTahlIQAVAAGI 239
Cdd:NF041036  168 FVSAPSLGLPTPNVTLERLLELCL---ITRRDGCS---SRDLLRRNLAEQGRDLDdfrrvvvsddlrLT---IQTVLDGG 238

                         250       260
                  ....*....|....*....|
gi 1502692554 240 GIALVPRILVQDEISSGELV 259
Cdd:NF041036  239 GISFVSRSLVCEYLKNGQLR 258
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 4-294 5.89e-84

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 254.38  E-value: 5.89e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   4 RRLtPSMSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIR 83
Cdd:PRK11139    3 RRL-PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  84 SATLQTIAhKSEGGTLHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMNAVICAGTGHWPGYVAH 163
Cdd:PRK11139   82 EATRKLRA-RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPD--IDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 164 PLIAEKLVLIASPSALPGHQAM-TPAEVAQHSLLGVVSRpNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIA 242
Cdd:PRK11139  159 KLLDEYLLPVCSPALLNGGKPLkTPEDLARHTLLHDDSR-EDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVA 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1502692554 243 LVPRILVQDEISSGELVTLF-EPMDSGRNYYLVYATRFQNLPSLCVFRDWLLS 294
Cdd:PRK11139  238 LGNRVLAQPEIEAGRLVCPFdTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLA 290
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 98-292 1.41e-59

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: 188.66  E-value: 1.41e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPS 177
Cdd:cd08481     1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDF--SQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 178 ALPGHQAMTPAEVAQHSLLGVVSRPNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSGE 257
Cdd:cd08481    79 LLAGRALAAPADLAHLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGR 158

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1502692554 258 LVTLFE-PMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08481   159 LVVPFNlPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 98-292 7.37e-56

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: 178.93  E-value: 7.37e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPS 177
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDF--AREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 178 ALPGHQAMTPAEVAQHSLLGVVSRPNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSGE 257
Cdd:cd08432    79 LLAGLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGR 158

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1502692554 258 LVTLFE-PMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08432   159 LVRPFDlPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-294 3.09e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.97  E-value: 3.09e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIRSATLQTIA 91
Cdd:COG0583     5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  92 HKSE-GGTLHLAVLPTFGSKWLLPRMHDFYARHPD---HVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIA 167
Cdd:COG0583    85 LRGGpRGTLRIGAPPSLARYLLPPLLARFRARHPGvrlELREGNSDRLVDAL--LEGELDLAIRLGPPPDPGLVARPLGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 168 EKLVLIASPsalpghqamtpaevaqhsllgvvsrpnawsdwfdrnqlDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRI 247
Cdd:COG0583   163 ERLVLVASP--------------------------------------DHPLARRAPLVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1502692554 248 LVQDEISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRDWLLS 294
Cdd:COG0583   205 LAADELAAGRLVALpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
1-295 2.28e-40

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 142.83  E-value: 2.28e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   1 MNPRRLTPS-MSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAAL 79
Cdd:PRK10086    6 MRNRLLNGWqLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  80 GRIrSATLQTIAHKSEGGTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLtpATSEMNAVICAGTGHWPG 159
Cdd:PRK10086   86 DTL-NQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNF--QRAGIDLAIYFDDAPSAQ 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 160 YVAHPLIAEKLVLIASPSALPGHQAM-TPAEVAQHSLL------GVVSRPNAWSDWFDRNQLDHHIMRPGPSFELTAHLI 232
Cdd:PRK10086  163 LTHHFLMDEEILPVCSPEYAERHALTgNPDNLRHCTLLhdrqawSNDSGTDEWHSWAQHFGVNLLPPSSGIGFDRSDLAV 242

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1502692554 233 QAVAAGIGIALVPRILVQDEISSGELVTLFEPMD--SGRNYYLVYATRFQNlPSLCVFRDWLLSI 295
Cdd:PRK10086  243 IAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEvkCHQHYYVTTLPGRQW-PKIEAFIDWLKEQ 306
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-293 9.25e-28

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: 106.60  E-value: 9.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLTP-ATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIAS 175
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLlLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 176 PS-ALPGHQAMTPAEVAQHSLLgVVSRPNAWSDWFDRNQLDHHI-MRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEI 253
Cdd:pfam03466  82 PDhPLARGEPVSLEDLADEPLI-LLPPGSGLRDLLDRALRAAGLrPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1502692554 254 SSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRDWLL 293
Cdd:pfam03466 161 ADGRLVALpLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 99-292 2.95e-25

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: 99.73  E-value: 2.95e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHPD-HVVHVHSRIVhADLTPATSEMnaVICAGTGHWPGYVAHPLIAEKLVLIASPS 177
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEiELSLLPSADL-VDLRPDGIDV--AIRYGNGDWPGLESEPLTAAPFVVVAAPG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 178 ALPGHQAMTPAEVAQHSLLGVVSRPNAWsDWFDRNQLDHHiMRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSGE 257
Cdd:cd08483    79 LLGDRKVDSLADLAGLPWLQERGTNEQR-VWLASMGVVPD-LERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGR 156

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1502692554 258 LVTLFEPMDSGRNYYLVyaTRFQNL-PSLCVFRDWL 292
Cdd:cd08483   157 LTVLFEEEEEGLGYHIV--TRPGVLrPAAKAFVRWL 190
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 99-292 2.05e-24

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: 97.44  E-value: 2.05e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHP--DHVVHVHSRIVHadltPATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASP 176
Cdd:cd08484     2 LTVGAVGTFAVGWLLPRLAEFRQLHPfiDLRLSTNNNRVD----IAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 177 SALPghQAMTPAEVAQHSLLGVVsRPNAWSDWFDRNQLDHHIMRpGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSG 256
Cdd:cd08484    78 ELAR--RLSEPADLANETLLRSY-RADEWPQWFEAAGVPPPPIN-GPVFDSSLLMVEAALQGAGVALAPPSMFSRELASG 153

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1502692554 257 ELVTLFEPMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08484   154 ALVQPFKITVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 99-292 8.87e-24

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


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 95.68  E-value: 8.87e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHP--DHVVHVHSRIVhadlTPATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASP 176
Cdd:cd08488     2 LHVGAVGTFAVGWLLPRLADFQNRHPfiDLRLSTNNNRV----DIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 177 SAlpGHQAMTPAEVAQHSLLGVVsRPNAWSDWFDRNQLDHHIMRP-GPSFELTAHLIQAVAAGIGIALVPRILVQDEISS 255
Cdd:cd08488    78 EL--ARQLREPADLARHTLLRSY-RADEWPQWFEAAGVGHPCGLPnSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLAS 154

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1502692554 256 GELVTLFEPMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08488   155 GALVQPFATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 97-292 5.22e-22

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: 90.96  E-value: 5.22e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPD-HV-VHVHSRIVhaDLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIA 174
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDvRLeLVLSDRLV--DL--VEEGFDLAIRIGELPDSSLVARRLGPVRRVLVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 175 SPSALPGHQA-MTPAEVAQHSLLGVvSRPNAWSDW-FDRNQLDHHImRPGPSFEL--TAHLIQAVAAGIGIALVPRILVQ 250
Cdd:cd08422    77 SPAYLARHGTpQTPEDLARHRCLGY-RLPGRPLRWrFRRGGGEVEV-RVRGRLVVndGEALRAAALAGLGIALLPDFLVA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1502692554 251 DEISSGELVTLFEP-MDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08422   155 EDLASGRLVRVLPDwRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-290 6.34e-22

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 93.07  E-value: 6.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   1 MNPRRLTpsmslliAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAG-ALYQH------ 73
Cdd:NF040786    1 MNLKQLE-------AFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGkLLYEYakemld 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  74 ---ELAAALGRIRsatlqtiahKSEGGTLHLAVlPTFGSKWLLPRM-HDFYARHPDHVVHV---HSRIVHADLtpatSEM 146
Cdd:NF040786   74 lweKLEEEFDRYG---------KESKGVLRIGA-STIPGQYLLPELlKKFKEKYPNVRFKLmisDSIKVIELL----LEG 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 147 NAVIcAGTGHWP---GYVAHPLIAEKLVLIAsPSALPGHQAMTPAEVAQHsllgVVSRPNAW----SDwfDRNQLDHHIM 219
Cdd:NF040786  140 EVDI-GFTGTKLekkRLVYTPFYKDRLVLIT-PNGTEKYRMLKEEISISE----LQKEPFIMreegSG--TRKEAEKALK 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 220 RPG---------PSFELTAHLIQAVAAGIGIALVPRILVQDEISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFR 289
Cdd:NF040786  212 SLGisledlnvvASLGSTEAIKQSVEAGLGISVISELAAEKEVERGRVLIFpIPGLPKNRDFYLVYNKNRQLSPTAEAFL 291


                  .
gi 1502692554 290 D 290
Cdd:NF040786  292 Q 292
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 7.87e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 7.87e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1502692554  10 MSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAG 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 99-292 1.20e-21

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: 90.15  E-value: 1.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMNAVICAGTGHWP-GYVAHPLIAEKLVLIASPS 177
Cdd:cd08482     2 LVLSCSGSLLMRWLIPRLPAFQAALPD--IDLQLSASDGPVDSLRDGIDAAIRFNDAPWPaGMQVIELFPERVGPVCSPS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 178 ALPGHQAMT--PAEVAQHSLLGVVSRPNAWSDWFDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEISS 255
Cdd:cd08482    80 LAPTVPLRQapAAALLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLAS 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1502692554 256 GELVTLFEPMDSGRNYYLVYATRFqNLPSLCVFRDWL 292
Cdd:cd08482   160 GRLVAPWGFIETGSHYVLLRPARL-RDSRAGALADWL 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 16-195 2.77e-20

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 88.47  E-value: 2.77e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  16 FEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQ-------HELAAALGRIRS-ATL 87
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLryarralQDLEAGRRAIHDvADL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  88 QTiahksegGTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHV----HSRIvHADLtpATSEMNAVICAGTGHWPGYVAH 163
Cdd:PRK11242   89 SR-------GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIremsQERI-EALL--ADDELDVGIAFAPVHSPEIEAQ 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1502692554 164 PLIAEKLVLIASPS-ALPGHQ-AMTPAEVAQHSL 195
Cdd:PRK11242  159 PLFTETLALVVGRHhPLAARRkALTLDELADEPL 192
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 99-292 7.71e-20

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: 84.90  E-value: 7.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPSA 178
Cdd:cd08487     2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDL--ATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 179 LPGHQamTPAEVAQHSLLGVVsRPNAWSDWFDRNQLDHHIMRpGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSGEL 258
Cdd:cd08487    80 AKRLS--HPADLINETLLRSY-RTDEWLQWFEAANMPPIKIR-GPVFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQL 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1502692554 259 VTLFEPMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08487   156 VQPFKIEVETGSYWLTWLKSKPMTPAMELFRQWI 189
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 98-292 2.16e-17

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: 78.41  E-value: 2.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPD---HVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIA 174
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGvelSLVEGGSSELLEAL--LEGELDLAIVALPVDDPGLESEPLFEEPLVLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 175 SPS-ALPGHQAMTPAEVAQHSLLgVVSRPNAWSDWFDRnQLDHHIMRPGPSFELTAH--LIQAVAAGIGIALVPRILVQd 251
Cdd:cd05466    79 PPDhPLAKRKSVTLADLADEPLI-LFERGSGLRRLLDR-AFAEAGFTPNIALEVDSLeaIKALVAAGLGIALLPESAVE- 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1502692554 252 EISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd05466   156 ELADGGLVVLpLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
23-283 1.04e-16

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 78.65  E-value: 1.04e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  23 GSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIRSATLQTIA-HKSEGGTLHL 101
Cdd:PRK10632   17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAfNNTPIGTLRI 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 102 AVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLTpaTSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPSALPG 181
Cdd:PRK10632   97 GCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLI--ADGLDVVIRVGALQDSSLFSRRLGAMPMVVCAAKSYLAQ 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 182 H-QAMTPAEVAQHSLLGVVSRPNAwsdwfdrnqlDHHIMRP-GPSFELTAH----------LIQAVAAGIGIALVPRILV 249
Cdd:PRK10632  175 YgTPEKPADLSSHSWLEYSVRPDN----------EFELIAPeGISTRLIPQgrfvtndpqtLVRWLTAGAGIAYVPLMWV 244

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1502692554 250 QDEISSGELVTLFEPMDSG-RNYYLVYATRfQNLP 283
Cdd:PRK10632  245 IDEINRGELEILFPRYQSDpRPVYALYTEK-DKLP 278
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-292 6.71e-16

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: 74.57  E-value: 6.71e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 106 TFGSKWLLPRMHDFYARHPDHVVHVH--SRIVhaDLTPATSEmnAVICAGTGHWPGYVAHPLIAEKLVLIASPSALPGHQ 183
Cdd:cd08477    10 TFGSHVLTPALAEYLARYPDVRVDLVlsDRLV--DLVEEGFD--AAFRIGELADSSLVARPLAPYRMVLCASPDYLARHG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 184 A-MTPAEVAQHSLLGVvSRPNAWSDWFDRNQLDHHIMRPGPSFEL--TAHLIQAVAAGIGIALVPRILVQDEISSGELVT 260
Cdd:cd08477    86 TpTTPEDLARHECLGF-SYWRARNRWRLEGPGGEVKVPVSGRLTVnsGQALRVAALAGLGIVLQPEALLAEDLASGRLVE 164

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1502692554 261 LF-EPMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08477   165 LLpDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-275 1.11e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 75.49  E-value: 1.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  16 FEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYqheLAAALGRIRSATLQTIAHKSE 95
Cdd:PRK10837   11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLL---YPRALALLEQAVEIEQLFRED 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  96 GGTLHLAVLPTFGSkWLLPRMHDFYARH-PDHVVHVH---SRivhaDLTPATSEMNAVI--CAGTGHWPGYVAHPLIAEK 169
Cdd:PRK10837   88 NGALRIYASSTIGN-YILPAMIARYRRDyPQLPLELSvgnSQ----DVINAVLDFRVDIglIEGPCHSPELISEPWLEDE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 170 LVLIASPSALPGHQAMTPAEVAQhsllgvvsrpnawSDWFDRNQ-------LDHHIMRPGPSFELTAHL-----IQ-AVA 236
Cdd:PRK10837  163 LVVFAAPDSPLARGPVTLEQLAA-------------APWILRERgsgtreiVDYLLLSHLPRFELAMELgnseaIKhAVR 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1502692554 237 AGIGIALVPRILVQDEISSGELVTLFEPMDS-GRNYYLVY 275
Cdd:PRK10837  230 HGLGISCLSRRVIADQLQAGTLVEVAVPLPRlMRTLYRIH 269
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-295 1.46e-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 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: 73.70  E-value: 1.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLTpatSE-MNAVICAGTGHWPGYVAHPLIAEKLVLIAS 175
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLI---REgVDCVIRVGELADSSLVARRLGELRMVTCAS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 176 PSALPGHQA-MTPAEVAQHSLLGVVS----RPNAWSdwFDRNQLDHHI-MRPGPSF-ELTAHLiQAVAAGIGIALVPRIL 248
Cdd:cd08472    78 PAYLARHGTpRHPEDLERHRAVGYFSartgRVLPWE--FQRDGEEREVkLPSRVSVnDSEAYL-AAALAGLGIIQVPRFM 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1502692554 249 VQDEISSGELVTLF-----EPMDsgrnYYLVYATRFQNLPSLCVFRDWLLSI 295
Cdd:cd08472   155 VRPHLASGRLVEVLpdwrpPPLP----VSLLYPHRRHLSPRVRVFVDWVAEL 202
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 12-261 2.65e-15

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 74.57  E-value: 2.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRdGRRIELTTAG----------ALYQHELAAALGR 81
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGqrllrharqvRLLEAELLAELPG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  82 IRSATLQTIAhkseggtlhLAV----LPTfgskWLLPRMHDFYARHP-------DHVVHVHSRIVHADLTPA-TSEMNAV 149
Cdd:TIGR03298  84 LAPGAPTRLT---------IAVnadsLAT----WFLPALAPVLAREGvlldlvvEDQDHTAELLRSGEVLGAvTTEAKPV 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 150 icagtghwPGYVAHPLIAEKLVLIASPSAlpgHQAMTPAEVAQHSLLG----VVSRPNAWSDWFDRNQLDHHIMRPG--- 222
Cdd:TIGR03298 151 --------PGCRVVPLGAMRYLAVASPAF---AARYFPDGVTAAALARapviVFNRKDDLQDRFLRRLFGLPVSPPRhyv 219

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1502692554 223 PSfelTAHLIQAVAAGIGIALVPRILVQDEISSGELVTL 261
Cdd:TIGR03298 220 PS---SEGFVDAARAGLGWGMVPELQAEPHLAAGRLVEL 255
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-135 2.06e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.97  E-value: 2.06e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  13 LIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALyqheLAAALGRIRSAT------ 86
Cdd:CHL00180   10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGEL----LLRYGNRILALCeetcra 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1502692554  87 ---LQTIahksEGGTLHLAVLPTFGsKWLLPRMHDFYA-RHPD-HV-VHVHS-RIV 135
Cdd:CHL00180   86 ledLKNL----QRGTLIIGASQTTG-TYLMPRLIGLFRqRYPQiNVqLQVHStRRI 136
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 98-290 2.87e-14

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: 69.83  E-value: 2.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVH---SRIVHADLTPATSEMnAVIcAGTGHWPGYVAHPLIAEKLVLIA 174
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTignTEEIAERVLDGEIDL-GLV-EGPVDHPDLIVEPFAEDELVLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 175 SPS-ALPGHQAMTPAEVAQHSLL------GVvsrpnawsdwfdRNQLDHHIMRPG-------PSFEL--TAHLIQAVAAG 238
Cdd:cd08420    79 PPDhPLAGRKEVTAEELAAEPWIlrepgsGT------------REVFERALAEAGldgldlnIVMELgsTEAIKEAVEAG 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1502692554 239 IGIALVPRILVQDEISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRD 290
Cdd:cd08420   147 LGISILSRLAVRKELELGRLVALpVEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-261 1.30e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 69.61  E-value: 1.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  10 MSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRdGRRIELTTAG-ALYQHELAAALgrIRSATLQ 88
Cdd:PRK13348    4 YKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGqRLLRHLRQVAL--LEADLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  89 TIAHKSEGG-TLHLAVLPTFGSKWLLPRMHDFYARHP---DHVV----HVHSRIVHADLTPA-TSEMNAVIcagtghwpG 159
Cdd:PRK13348   81 TLPAERGSPpTLAIAVNADSLATWFLPALAAVLAGERillELIVddqdHTFALLERGEVVGCvSTQPKPMR--------G 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 160 YVAHPLIAEKLVLIASPSAlpgHQAMTPAEVAQHSLLG----VVSRPNAWSDWFDRNQLDHHIMR------PGPSfeltA 229
Cdd:PRK13348  153 CLAEPLGTMRYRCVASPAF---AARYFAQGLTRHSALKapavAFNRKDTLQDSFLEQLFGLPVGAyprhyvPSTH----A 225

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1502692554 230 HLiQAVAAGIGIALVPRILVQDEISSGELVTL 261
Cdd:PRK13348  226 HL-AAIRHGLGYGMVPELLIGPLLAAGRLVDL 256
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 19-259 2.92e-13

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: 68.61  E-value: 2.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  19 AARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGrIRSATLQTIAHKSEGGT 98
Cdd:NF041036   12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILD-IEDSLMDELKSFKGRQR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  99 LHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMN-----AVI--CAGTGHWPgYVAHPLIAEKLV 171
Cdd:NF041036   91 LSICCTPTFGMAHLPGVLNRFMLRNAD--VVDLKFLFHSPAQALEGIQNkefdlAIIehCADLDLGR-FHTYPLPQDELV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 172 LIASPSALPGHQAMTPAEVAQHSLlgvVSRPNAWSdwfDRNQLDHHIMRPGPSFE------------LTahlIQAVAAGI 239
Cdd:NF041036  168 FVSAPSLGLPTPNVTLERLLELCL---ITRRDGCS---SRDLLRRNLAEQGRDLDdfrrvvvsddlrLT---IQTVLDGG 238

                         250       260
                  ....*....|....*....|
gi 1502692554 240 GIALVPRILVQDEISSGELV 259
Cdd:NF041036  239 GISFVSRSLVCEYLKNGQLR 258
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
12-261 3.92e-13

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 68.26  E-value: 3.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRdGRRIELTTAG----------ALYQHELAAALGR 81
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGqrllrharqvRLLEAELLGELPA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  82 IRSATLqtiahkseggTLHLAV----LPTfgskWLLPRMHDFYARHP---DHVV----HVHSRIVHADLTPA-TSEMNAV 149
Cdd:PRK03635   85 LDGTPL----------TLSIAVnadsLAT----WFLPALAPVLARSGvllDLVVedqdHTAELLRRGEVVGAvTTEPQPV 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 150 icagtghwPGYVAHPLIAEKLVLIASpsalpghqamtPAEVAQHSLLGVvsRPNAWSDW----FDRNQLDHH-----IMR 220
Cdd:PRK03635  151 --------QGCRVDPLGAMRYLAVAS-----------PAFAARYFPDGV--TAEALAKApavvFNRKDDLQDrflrqAFG 209

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1502692554 221 PGPSFELTaHLI-------QAVAAGIGIALVPRILVQDEISSGELVTL 261
Cdd:PRK03635  210 LPPGSVPC-HYVpsseafvRAALAGLGWGMIPELQIEPELASGELVDL 256
PRK09986 PRK09986
LysR family transcriptional regulator;
9-245 1.36e-12

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 66.67  E-value: 1.36e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   9 SMSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAaalgRIRSATLQ 88
Cdd:PRK09986    8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESR----RLLDNAEQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  89 TIAH-----KSEGGTLHLAVLPTfgSKW--LLPRMHDFYARHPDHVVHVHsrivhaDLTPATS-------EMNAVI--CA 152
Cdd:PRK09986   84 SLARveqigRGEAGRIEIGIVGT--ALWgrLRPAMRHFLKENPNVEWLLR------ELSPSMQmaalerrELDAGIwrMA 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 153 GTGHWPGYVAHpLIAEKLVLIASP--SALPGHQAMTPAEVAQHSLlgvVSRPNAWSDW--FDRNQLDHHIMRPGPSFELT 228
Cdd:PRK09986  156 DLEPNPGFTSR-RLHESAFAVAVPeeHPLASRSSVPLKALRNEYF---ITLPFVHSDWgkFLQRVCQQAGFSPQIIRQVN 231

                         250
                  ....*....|....*....
gi 1502692554 229 --AHLIQAVAAGIGIALVP 245
Cdd:PRK09986  232 epQTVLAMVSMGIGITLLP 250
PRK09801 PRK09801
LysR family transcriptional regulator;
23-275 7.24e-12

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 64.67  E-value: 7.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  23 GSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGA-LYQH--ELAAALGRIRSATLQtIAHKSEGgTL 99
Cdd:PRK09801   21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrCYEHalEILTQYQRLVDDVTQ-IKTRPEG-MI 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 100 HLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLTPATSEMNAVICAGTGHWpgYVAHPLIAEKLVLIASPSAL 179
Cdd:PRK09801   99 RIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDY--YIAHLLTKNKRILCAAPEYL 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 180 PGH-QAMTPAEVAQHSLLGVVSRPNAWSDWFDRNQLDHHimrpgpSFELTAHL--------IQAVAAGIGIALVPRILVQ 250
Cdd:PRK09801  177 QKYpQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKK------SVKVSGHLssnsgeivLQWALEGKGIMLRSEWDVL 250

                         250       260
                  ....*....|....*....|....*
gi 1502692554 251 DEISSGELVTLFEPMDSGRNYYLVY 275
Cdd:PRK09801  251 PFLESGKLVQVLPEYAQSANIWAVY 275
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
13-260 7.80e-12

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 64.65  E-value: 7.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  13 LIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIRSAtLQTiAH 92
Cdd:PRK15421    7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA-LQA-CN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  93 KSEGGTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHaDLTPA--TSEMNAVICAGTGHWPGYVAHPLIAEKL 170
Cdd:PRK15421   85 EPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTF-DPQPAlqQGELDLVMTSDILPRSGLHYSPMFDYEV 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 171 VLIASPS-ALPGHQAMTPAEVAQHSLLgvvSRPnawsdwFDRNQLD--HHIMRPG------PSFELTAHLIQAVAAGIGI 241
Cdd:PRK15421  164 RLVLAPDhPLAAKTRITPEDLASETLL---IYP------VQRSRLDvwRHFLQPAgvspslKSVDNTLLLIQMVAARMGI 234

                         250
                  ....*....|....*....
gi 1502692554 242 ALVPRILVQDEISSGELVT 260
Cdd:PRK15421  235 AALPHWVVESFERQGLVVT 253
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 16-292 3.02e-11

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 63.09  E-value: 3.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  16 FEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIRSATLQTIAHKSE 95
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  96 G-GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHSRIVHADLTpatsemnavicaGTGHWPGYVAHPLIAEKLVLIA 174
Cdd:PRK14997   90 PrGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVV------------GEGVDVAIRVRPRPFEDSDLVM 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 175 SPSALPGHQAM-TPAEVAQhslLGVVSRPNAWSDW----FDRNQLDHHIMRPGP-----SFELTAHLI--------QAVA 236
Cdd:PRK14997  158 RVLADRGHRLFaSPDLIAR---MGIPSAPAELSHWpglsLASGKHIHRWELYGPqgaraEVHFTPRMIttdmlalrEAAM 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1502692554 237 AGIGIALVPRILVQDEISSGELVTLFEPMDSGRNY-YLVYATRFQNLPSLCVFRDWL 292
Cdd:PRK14997  235 AGVGLVQLPVLMVKEQLAAGELVAVLEEWEPRREViHAVFPSRRGLLPSVRALVDFL 291
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 17-131 3.51e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 62.65  E-value: 3.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  17 EAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGR---IRSATlQTIAHk 93
Cdd:PRK11074   11 DAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKmqeTRRQC-QQVAN- 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1502692554  94 seG--GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVH 131
Cdd:PRK11074   89 --GwrGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIR 126
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-245 2.08e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.38  E-value: 2.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   1 MNPRRLTpsmslliAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGA-LYQHelAAAL 79
Cdd:PRK11233    1 MNFRRLK-------YFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKiLYTH--ARAI 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  80 grIRSATLQTIAHKSEGGTLHLAV----LP-TFGSKWLLPRMHDFYARHPDHVVHVHSrivhaDLTPATSE--MN----- 147
Cdd:PRK11233   72 --LRQCEQAQLAVHNVGQALSGQVsiglAPgTAASSLTMPLLQAVRAEFPGIVLYLHE-----NSGATLNEklMNgqldm 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 148 AVIcagTGHWP--GYVAHPLIAEKLVLIaSPSALPGhQAMTPAEVAQHSLLgvVSRP-NAWsdwfdRNQLDHHIMRPGPS 224
Cdd:PRK11233  145 AVI---YEHSPvaGLSSQPLLKEDLFLV-GTQDCPG-QSVDLAAVAQMNLF--LPRDySAV-----RLRVDEAFSLRRLT 212

                         250       260
                  ....*....|....*....|....*..
gi 1502692554 225 ------FELTAHLIQAVAAGIGIALVP 245
Cdd:PRK11233  213 akvigeIESIATLTAAIASGMGVTVLP 239
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 18-143 3.39e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 56.92  E-value: 3.39e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  18 AAARHG-SFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIE-LTTAGalyQHELAAA------LGRIRSATLQT 89
Cdd:PRK12682   11 EAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPG---KAVLDVIerilreVGNIKRIGDDF 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1502692554  90 IAhkSEGGTLHLAVLPTfGSKWLLPR-MHDFYARHPDHVVHVH-------SRIV---HADLTPAT 143
Cdd:PRK12682   88 SN--QDSGTLTIATTHT-QARYVLPRvVAAFRKRYPKVNLSLHqgspdeiARMVisgEADIGIAT 149
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-267 2.23e-08

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: 53.33  E-value: 2.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVH--SRIV-----HADLtpatsemnAVICAGTGHWPGYVAHPLIAEK 169
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSfsDRFVdlieeGIDL--------AVRIGELADSTGLVARRLGTQR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 170 LVLIASPSALPGH-QAMTPAEVAQHSLL--GVVSRPNAWsdwfdrnqldhHIMRPGPS---FELTAHL--------IQAV 235
Cdd:cd08475    73 MVLCASPAYLARHgTPRTLEDLAEHQCIayGRGGQPLPW-----------RLADEQGRlvrFRPAPRLqfddgeaiADAA 141

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1502692554 236 AAGIGIALVPRILVQDEISSGELVTLFEPMDS 267
Cdd:cd08475   142 LAGLGIAQLPTWLVADHLQRGELVEVLPELAP 173
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
21-68 4.81e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 53.10  E-value: 4.81e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1502692554  21 RHgsFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAG 68
Cdd:PRK03601   16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 16-132 8.03e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 52.46  E-value: 8.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  16 FEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALGRIRSATLQTIAHKSE 95
Cdd:PRK09906    9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE 88

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1502692554  96 GGTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHS 132
Cdd:PRK09906   89 DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVS 125
nhaR PRK11062
transcriptional activator NhaR; Provisional
 23-70 8.26e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 52.70  E-value: 8.26e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1502692554  23 GSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGAL 70
Cdd:PRK11062   19 GSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGEL 66
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-292 1.18e-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 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: 51.31  E-value: 1.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDhvvhvhsriVHADLTpATSEMNAVICAG------TGhwpGYVAHPLIA--- 167
Cdd:cd08474     3 GTLRINAPRVAARLLLAPLLARFLARYPD---------IRLELV-VDDGLVDIVAEGfdagirLG---ESVEKDMVAvpl 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 168 ---EKLVLIASPSALPGHQA-MTPAEVAQHSLLG----VVSRPNAWSdwFDRNQLDHHIMRPGP-SFELTAHLIQAVAAG 238
Cdd:cd08474    70 gppLRMAVVASPAYLARHGTpEHPRDLLNHRCIRyrfpTSGALYRWE--FERGGRELEVDVEGPlILNDSDLMLDAALDG 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1502692554 239 IGIALVPRILVQDEISSGELVTLFE---PMDSGrnYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08474   148 LGIAYLFEDLVAEHLASGRLVRVLEdwsPPFPG--GYLYYPSRRRVPPALRAFIDFL 202
PRK10341 PRK10341
transcriptional regulator TdcA;
6-96 1.68e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.79  E-value: 1.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   6 LTPSMSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGAL-------YQHELAAA 78
Cdd:PRK10341    5 LLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVllsrsesITREMKNM 84

                          90
                  ....*....|....*...
gi 1502692554  79 LGRIRSATLQTIAHKSEG 96
Cdd:PRK10341   85 VNEINGMSSEAVVDVSFG 102
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 97-261 3.48e-07

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 49.83  E-value: 3.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSkWLLPR-MHDFYARHPD---HVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVL 172
Cdd:cd08411     1 GPLRLGVIPTIAP-YLLPRlLPALRQAYPKlrlYLREDQTERLLEKL--RSGELDAALLALPVDEPGLEEEPLFDEPFLL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 173 IASPS-ALPGHQAMTPAEVAQHSLLGvvsrpnawsdwfdrnqLDH-HIMR-----------PGPSFELTAH----LIQAV 235
Cdd:cd08411    78 AVPKDhPLAKRKSVTPEDLAGERLLL----------------LEEgHCLRdqalelcrlagAREQTDFEATsletLRQMV 141

                         170       180
                  ....*....|....*....|....*.
gi 1502692554 236 AAGIGIALVPRILVQDEISSGELVTL 261
Cdd:cd08411   142 AAGLGITLLPELAVPSEELRGDRLVV 167
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-78 5.51e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 50.19  E-value: 5.51e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1502692554   5 RLTPSMslLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGalyQHELAAA 78
Cdd:PRK10094    1 MFDPET--LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAG---EHLLSQA 69
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-114 7.52e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 49.64  E-value: 7.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554   1 MNPRRLtpsmSLLIAFeaaARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAALG 80
Cdd:PRK11151    1 MNIRDL----EYLVAL---AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLR 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1502692554  81 RIRsaTLQTIAH---KSEGGTLHLAVLPTFGSkWLLP 114
Cdd:PRK11151   74 EVK--VLKEMASqqgETMSGPLHIGLIPTVGP-YLLP 107
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 112-264 7.63e-07

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: 48.87  E-value: 7.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 112 LLPRMHDFYARHPDHVVHVHSRIVHADLTpaTSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPSALPGHQA-MTPAEV 190
Cdd:cd08478    18 LAPLIAKFRERYPDIELELVSNEGIIDLI--ERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHGTpQSIEDL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1502692554 191 AQHSLLGVvSRPNAWSDW-FDRNQLDHHIMRPGPSFELTAHLIQAVAAGIGIALVPRILVQDEISSGELVTLFEP 264
Cdd:cd08478    96 AQHQLLGF-TEPASLNTWpIKDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFAE 169
PRK09791 PRK09791
LysR family transcriptional regulator;
13-83 1.02e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 49.38  E-value: 1.02e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1502692554  13 LIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAG-ALYQH------ELAAALGRIR 83
Cdd:PRK09791   10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGeSFYQHaslileELRAAQEDIR 87
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-268 1.59e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 47.72  E-value: 1.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 107 FGSKWLLPRMHDFYARHPDHVVHvhsrIVHADLTPATSEMNAVICAGTGHWP--GYVAHPLIAEKLVLIASPSALPGH-Q 183
Cdd:cd08480    11 FGTHFLLPLLPAFLARYPEILVD----LSLTDEVVDLLAERTDVAIRVGPLPdsSLVARKLGESRRVIVASPSYLARHgT 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 184 AMTPAEVAQHSLLGVVSRPNAwSDW-FDRNQLDHHIMRPGPSFELTAHLIQAVA-AGIGIALVPRILVQDEISSGELVTL 261
Cdd:cd08480    87 PLTPQDLARHNCLGFNFRRAL-PDWpFRDGGRIVALPVSGNILVNDGEALRRLAlAGAGLARLALFHVADDIAAGRLVPV 165


                  ....*..
gi 1502692554 262 FEPMDSG 268
Cdd:cd08480   166 LEEYNPG 172
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
37-73 1.83e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 48.28  E-value: 1.83e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1502692554  37 SAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQH 73
Cdd:PRK11716    6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRP 42
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 16-130 2.00e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 48.45  E-value: 2.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  16 FEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQHELAAA---LGRIRSATlQTIaH 92
Cdd:PRK11013   12 FHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAA-ESL-R 89

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1502692554  93 KSEGGTLHLAVLPTFgSKWLLPRM-HDFYARHPDHVVHV 130
Cdd:PRK11013   90 EFRQGQLSIACLPVF-SQSLLPGLcQPFLARYPDVSLNI 127
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 12-68 2.30e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 48.10  E-value: 2.30e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAG 68
Cdd:PRK15092   15 LLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 161-292 2.34e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 47.16  E-value: 2.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 161 VAHPLIAEKLVLIASPSALPGHQAMTPAEVAQHSLLGVVSRPNAwsdwfdRNQLDHhimRPG-PSFELTAhLIQAVAAGI 239
Cdd:cd08473    79 VASPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDGE------SITVRH---RPRlVTDDLLT-LRQAALAGV 148

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1502692554 240 GIALVPRILVQDEISSGELVTLFEPMDSGRN-YYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08473   149 GIALLPDHLCREALRAGRLVRVLPDWTPPRGiVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-261 4.66e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 46.44  E-value: 4.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHSRIVHADLTPATSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASP 176
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPE--LEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 177 SALPGH-QAMTPAEVAQHSLLGVVSRPNAWSDW-FDRNQLDHHIMRPGPSFELTAHLIQAVA-AGIGIALVPRILVQDEI 253
Cdd:cd08479    79 AYLERHgAPASPEDLARHDCLVIRENDEDFGLWrLRNGDGEATVRVRGALSSNDGEVVLQWAlDGHGIILRSEWDVAPYL 158


                  ....*...
gi 1502692554 254 SSGELVTL 261
Cdd:cd08479   159 RSGRLVRV 166
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
17-68 4.72e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 47.28  E-value: 4.72e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1502692554  17 EAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRI-ELTTAG 68
Cdd:PRK12684   11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPG 63
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
24-261 6.19e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 46.97  E-value: 6.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  24 SFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELTTAGALYQ-------HELAAALGRIRSAT--LQTIAHKS 94
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHsqirhllQQLESNLAELRGGSdyAQRKIKIA 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  95 EGGTLHLAVLPTFGSK------WLLPRM-------------HDF-YARHPDHVVHV---HSRIVHADLTPatsemnavIC 151
Cdd:PRK10082  107 AAHSLSLGLLPSIISQmpplftWAIEAIdvdeavdklregqSDCiFSFHDEDLLEApfdHIRLFESQLFP--------VC 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 152 AGTGHwpgyvahpliAEKLVLIASPsalpghqamtpaevaqHSLLGVVSRPNAWSDWFDRNQLDHHIMRPGPSF--ELTA 229
Cdd:PRK10082  179 ASDEH----------GEALFNLAQP----------------HFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFvsSMSE 232

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1502692554 230 HLIQAVAAGIGIALVPRILVQDEISSGELVTL 261
Cdd:PRK10082  233 LLKQVALDGCGIAWLPEYAIQQEIRSGQLVVL 264
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-264 1.25e-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 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: 45.21  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHV--HSRIV-----HADLtpatsemnAV-IcagtGHWP--GYVAHPLI 166
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLllLDRVVnlleeGVDV--------AVrI----GHLPdsSLVATRVG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 167 AEKLVLIASPSALPGHQA-MTPAEVAQHSLLGVVSRPNAwSDWFDRNQLDHHIMRPGPSFELT--AHLIQAVAAGIGIAL 243
Cdd:cd08471    69 SVRRVVCASPAYLARHGTpKHPDDLADHDCIAFTGLSPA-PEWRFREGGKERSVRVRPRLTVNtvEAAIAAALAGLGLTR 147

                         170       180
                  ....*....|....*....|....
gi 1502692554 244 VPRILVQDEISSGELVTL---FEP 264
Cdd:cd08471   148 VLSYQVAEELAAGRLQRVledFEP 171
cbl PRK12679
HTH-type transcriptional regulator Cbl;
12-62 1.38e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 45.96  E-value: 1.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRI 62
Cdd:PRK12679    6 LKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRL 56
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 98-292 1.54e-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: 44.81  E-value: 1.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTfgSKWLLPRM-HDFYARHPDhvVHVHSRI-----VHADLtpATSEMNAVIcagTGHWP---GYVAHPLIAE 168
Cdd:cd08419     1 RLRLAVVST--AKYFAPRLlGAFCRRHPG--VEVSLRVgnreqVLERL--ADNEDDLAI---MGRPPedlDLVAEPFLDN 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 169 KLVLIASPS-ALPGHQAMTPAEVAQHSLL----GVVSRpNAWSDWFDRnqldhHIMRPGPSFELTAH--LIQAVAAGIGI 241
Cdd:cd08419    72 PLVVIAPPDhPLAGQKRIPLERLAREPFLlrepGSGTR-LAMERFFAE-----HGVTLRVRMELGSNeaIKQAVMAGLGL 145

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1502692554 242 ALVPRILVQDEISSGELVTL-FEPMDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08419   146 SVLSLHTLALELATGRLAVLdVEGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-264 2.67e-05

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 44.05  E-value: 2.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVHsrivhaDlTPATSEMNAV--------ICAGTGHWPGYVAHPLIAEK 169
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLR------D-VSAEQVIEAVrsgevdfgIGSEPEADPDLEFEPLLRDP 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 170 LVLIASPS-ALPGHQAMTPAEVAQHSLLGvVSRPNAWSDWFDRNQLDHHImRPGPSFE--LTAHLIQAVAAGIGIALVPR 246
Cdd:cd08440    74 FVLVCPKDhPLARRRSVTWAELAGYPLIA-LGRGSGVRALIDRALAAAGL-TLRPAYEvsHMSTALGMVAAGLGVAVLPA 151

                         170
                  ....*....|....*....
gi 1502692554 247 ILVQDEISSG-ELVTLFEP 264
Cdd:cd08440   152 LALPLADHPGlVARPLTEP 170
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 12-62 2.74e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.03  E-value: 2.74e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRI 62
Cdd:PRK12683    6 LRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRL 56
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-249 7.37e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 42.95  E-value: 7.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 112 LLPR-MHDFYARHPDHVVHVhsrivhadlTPATS----------EMNAVICA--GTGHWPGYVAHPLIAEKLVLIAsPSA 178
Cdd:cd08427    14 LLPRaLARLRRRHPDLEVHI---------VPGLSaellarvdagELDAAIVVepPFPLPKDLVWTPLVREPLVLIA-PAE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 179 LPGHqamTPAEVAQ-HSLLGvvsrpnawsdwFDRNQ---------LDHHIMRPGPSFELTA--HLIQAVAAGIGIALVPR 246
Cdd:cd08427    84 LAGD---DPRELLAtQPFIR-----------YDRSAwggrlvdrfLRRQGIRVREVMELDSleAIAAMVAQGLGVAIVPD 149


                  ...
gi 1502692554 247 ILV 249
Cdd:cd08427   150 IAV 152
cysB PRK12681
HTH-type transcriptional regulator CysB;
26-131 2.08e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.19  E-value: 2.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  26 TKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRI-ELTTAGalyQHELAAA---LGRIRSatLQTIAH---KSEGGT 98
Cdd:PRK12681   20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAG---EEIIRIAreiLSKVES--IKSVAGehtWPDKGS 94

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1502692554  99 LHLAVLPTfGSKWLLPR-MHDFYARHPDHVVHVH 131
Cdd:PRK12681   95 LYIATTHT-QARYALPPvIKGFIERYPRVSLHMH 127
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 98-244 5.36e-04

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: 40.24  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKwLLPRM-HDFYARHPDHVVHVHSRIV----------HADLTPATSEMNAvicagtghwPGYVAHPLI 166
Cdd:cd08415     1 TLRIAALPALALS-LLPRAiARFRARHPDVRISLHTLSSstvveavlsgQADLGLASLPLDH---------PGLESEPLA 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 167 AEKLVLIASPS-ALPGHQAMTPAEVAQHSLLGVvsrpnAWSDWFdRNQLDHHIMRPG--PSFELTAHLIQA----VAAGI 239
Cdd:cd08415    71 SGRAVCVLPPGhPLARKDVVTPADLAGEPLISL-----GRGDPL-RQRVDAAFERAGvePRIVIETQLSHTacalVAAGL 144


                  ....*
gi 1502692554 240 GIALV 244
Cdd:cd08415   145 GVAIV 149
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-246 6.01e-04

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 40.28  E-value: 6.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPDhvVHVHsrivhadLTPATSEM-----------NAVICAGTGHWPGYVAHPLI 166
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPG--VDIR-------LRQAGSDDllaavregrldLAFVGLPERRPPGLASRELA 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 167 AEKLVLIASPS-ALPGHQAMTPAEVAQHSLLGVVSrpnawsDWFDRNQLDH----HIMRPGPSFELT--AHLIQAVAAGI 239
Cdd:cd08436    72 REPLVAVVAPDhPLAGRRRVALADLADEPFVDFPP------GTGARRQVDRafaaAGVRRRVAFEVSdvDLLLDLVARGL 145


                  ....*..
gi 1502692554 240 GIALVPR 246
Cdd:cd08436   146 GVALLPA 152
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 170-292 1.50e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 38.76  E-value: 1.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 170 LVLIASPSALPGH-QAMTPAEVAQHSLLGVVSrPNA--WSDWFDRNqldhhiMRPGPSFELTAH--------LIQAVAAG 238
Cdd:cd08476    70 MVLVASPDYLARHgTPETPADLAEHACLRYRF-PTTgkLEPWPLRG------DGGDPELRLPTAlvcnnieaLIEFALQG 142

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1502692554 239 IGIALVPRILVQDEISSGELVTLFEP-MDSGRNYYLVYATRFQNLPSLCVFRDWL 292
Cdd:cd08476   143 LGIACLPDFSVREALADGRLVTVLDDyVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
leuO PRK09508
leucine transcriptional activator; Reviewed
 12-65 1.94e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 39.24  E-value: 1.94e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1502692554  12 LLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIELT 65
Cdd:PRK09508   26 LLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT 79
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 98-246 4.28e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. 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: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 37.49  E-value: 4.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  98 TLHLAVLPTFGSKWLLPRMHDFYARHPD---HVVHVHSRIVHADLtpATSEMNAVICAGTGHWPGYVAHPLIAEKLVL-I 173
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDvelELREMTTAEQLEAL--RAGRLDVGFVRPPPDPPGLASRPLLREPLVVaL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1502692554 174 ASPSALPGHQAMTPAEVAQHSLlgVVSRPNAWSDWFDrnQLDHHIMRPG--PSFELTAHLIQA----VAAGIGIALVPR 246
Cdd:cd08414    79 PADHPLAARESVSLADLADEPF--VLFPREPGPGLYD--QILALCRRAGftPRIVQEASDLQTllalVAAGLGVALVPA 153
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-264 6.42e-03

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: 36.90  E-value: 6.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554  97 GTLHLAVLPTFGSKWLLPRMHDFYARHPDHVVHVH--SRIVhaDLTpatsEMNAVICAGTGHWPGyvaHPLIAEKL---- 170
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIEltNRVV--DLV----SEGFDLAIRLGRLTD---SSLMARRLasrr 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 171 -VLIASPSALPGHQA-MTPAEVAQHS-LLGvvSRPNawsdWfdRNQLDHHIMRPGPSFELTAH----LIQAVAAGIGIAL 243
Cdd:cd08470    72 hYVCASPAYLERHGTpHSLADLDRHNcLLG--TSDH----W--RFQENGRERSVRVQGRWRCNsgvaLLDAALKGMGLAQ 143

                         170       180
                  ....*....|....*....|.
gi 1502692554 244 VPRILVQDEISSGELVTLFEP 264
Cdd:cd08470   144 LPDYYVDEHLAAGRLVPVLED 164
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 111-261 7.20e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 36.78  E-value: 7.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 111 WLLPRMHDFYARHPDHVVHVHSRiVHADLTPA--TSEMNAVICAGTGHWPGYVAHPLIAEKLVLIASPS-ALPGHQAMTP 187
Cdd:cd08441    14 WLMPVLDQFRERWPDVELDLSSG-FHFDPLPAllRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDhPLAAKEFITP 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1502692554 188 AEVAQHSLLgvvSRPnawsdwFDRNQLDhhIMR---------PGP--SFELTAHLIQAVAAGIGIALVPRILVQDEISSG 256
Cdd:cd08441    93 EDLADETLI---TYP------VERERLD--VFRhflqpagiePKRrrTVELTLMILQLVASGRGVAALPNWAVREYLDQG 161


                  ....*
gi 1502692554 257 ELVTL 261
Cdd:cd08441   162 LVVAR 166
PRK11482 PRK11482
DNA-binding transcriptional regulator;
10-74 7.42e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 37.39  E-value: 7.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1502692554  10 MSLLIAFEAAARHGSFTKAADELALTQSAVSRQVQALEAQLEVELFKRDGRRIeLTTAGALYQHE 74
Cdd:PRK11482   31 LNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGV-TPTAYATHLHE 94
 
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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