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Conserved domains on  [gi|375137193|ref|YP_004997843|]
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LysR family transcriptional regulatory protein [Acinetobacter pittii PHEA-2]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426520)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic binding proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  8257110|19047729
SCOP:  3000083|4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 90-288 3.00e-44

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08433:

Pssm-ID: 473866  Cd Length: 198  Bit Score: 149.67  E-value: 3.00e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPK 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 170 EVMSEyhlesciDTQTINHSQLKELPLILPSQRHGLRLLLEQKIHQ----LKVAYEIDGLHLLMESISQLEMATIQPAGA 245
Cdd:cd08433   81 DAPLP-------RGAPVPLAELARLPLILPSRGHGLRRLVDEAAARagltLNVVVEIDSVATLKALVAAGLGYTILPASA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 375137193 246 --SLNSRQDLCLLRVVEPAIERINYLISLSEEELSPATLATKVVI 288
Cdd:cd08433  154 vaAEVAAGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-170 1.02e-43

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.02  E-value: 1.02e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHSSR--LSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPL 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170
                 ....*....|..
gi 375137193 159 VKEQMFLISPKE 170
Cdd:COG0583  161 GEERLVLVASPD 172
 
Name Accession Description Interval E-value
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 90-288 3.00e-44

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 149.67  E-value: 3.00e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPK 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 170 EVMSEyhlesciDTQTINHSQLKELPLILPSQRHGLRLLLEQKIHQ----LKVAYEIDGLHLLMESISQLEMATIQPAGA 245
Cdd:cd08433   81 DAPLP-------RGAPVPLAELARLPLILPSRGHGLRRLVDEAAARagltLNVVVEIDSVATLKALVAAGLGYTILPASA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 375137193 246 --SLNSRQDLCLLRVVEPAIERINYLISLSEEELSPATLATKVVI 288
Cdd:cd08433  154 vaAEVAAGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-170 1.02e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.02  E-value: 1.02e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHSSR--LSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPL 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170
                 ....*....|..
gi 375137193 159 VKEQMFLISPKE 170
Cdd:COG0583  161 GEERLVLVASPD 172
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-300 1.06e-33

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 125.18  E-value: 1.06e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHA-- 78
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAql 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  79 -VDSAHSSrLSGHVTVGFSPSVAA-VIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQ 156
Cdd:PRK11233  81 aVHNVGQA-LSGQVSIGLAPGTAAsSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQ 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 157 PLVKEQMFLISPKevmseyhleSCIDtQTINHSQLKELPLILPSQRHGLRLLLEQKIHQLKVAYEIDGlhlLMESISQLE 236
Cdd:PRK11233 160 PLLKEDLFLVGTQ---------DCPG-QSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIG---EIESIATLT 226

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 375137193 237 MA-------TIQPAGA--SLNSRQDLCLLRVVEPAIErinylISLS-----EEELSPATLATKVVIRACVTNLINEKR 300
Cdd:PRK11233 227 AAiasgmgvTVLPESAarSLCGAVNGWMARITTPSMS-----LSLSlnlsaRLPLSPQAQAVKEILLSLVSSPVMEKR 299
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-289 4.57e-23

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: 96.53  E-value: 4.57e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQ--LALRH-LDH 77
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKemLDLWEkLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  78 AVDSaHSSRLSGHVTVGFSpsvaAVIGTHFL----KLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQW 153
Cdd:NF040786  81 EFDR-YGKESKGVLRIGAS----TIPGQYLLpellKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 154 AIQPLVKEQMFLISPKEvMSEYHlescIDTQTINHSQLKELPLILPSQRHGLRLLLEQKIH-------QLKVAYEIDGLH 226
Cdd:NF040786 156 VYTPFYKDRLVLITPNG-TEKYR----MLKEEISISELQKEPFIMREEGSGTRKEAEKALKslgisleDLNVVASLGSTE 230

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375137193 227 LLMES---------ISQLematiqpAGASLNSRQDLCLLRVVEPAIERINYLISLSEEELSPATLATKVVIR 289
Cdd:NF040786 231 AIKQSveaglgisvISEL-------AAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-283 1.34e-21

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 90.43  E-value: 1.34e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   88 SGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLIS 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  168 PKevmsEYHLEsciDTQTINHSQLKELPLILPSQRHGLRLLLEQKIHQ----LKVAYEIDGLHLLMESISQLEMATIQPA 243
Cdd:pfam03466  81 PP----DHPLA---RGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrPRVVLEVNSLEALLQLVAAGLGIALLPR 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 375137193  244 GASLNSRQD--LCLLRVVEPAIERINYLISLSEEELSPATLA 283
Cdd:pfam03466 154 SAVARELADgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRA 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-159 1.18e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 81.35  E-value: 1.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHS-SRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLS-GDLKALVNArQLDVAI----IFSDDVDPQWA 154
Cdd:PRK09906  81 RARKiVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITtQQEEKLRRG-ELDVGFmrhpVYSDEIDYLEL 159


                 ....*.
gi 375137193 155 I-QPLV 159
Cdd:PRK09906 160 LdEPLV 165
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.82e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.96  E-value: 3.82e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 375137193    3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 90-288 3.00e-44

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 149.67  E-value: 3.00e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPK 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 170 EVMSEyhlesciDTQTINHSQLKELPLILPSQRHGLRLLLEQKIHQ----LKVAYEIDGLHLLMESISQLEMATIQPAGA 245
Cdd:cd08433   81 DAPLP-------RGAPVPLAELARLPLILPSRGHGLRRLVDEAAARagltLNVVVEIDSVATLKALVAAGLGYTILPASA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 375137193 246 --SLNSRQDLCLLRVVEPAIERINYLISLSEEELSPATLATKVVI 288
Cdd:cd08433  154 vaAEVAAGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-170 1.02e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.02  E-value: 1.02e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHSSR--LSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPL 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170
                 ....*....|..
gi 375137193 159 VKEQMFLISPKE 170
Cdd:COG0583  161 GEERLVLVASPD 172
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-300 1.06e-33

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 125.18  E-value: 1.06e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHA-- 78
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAql 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  79 -VDSAHSSrLSGHVTVGFSPSVAA-VIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQ 156
Cdd:PRK11233  81 aVHNVGQA-LSGQVSIGLAPGTAAsSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQ 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 157 PLVKEQMFLISPKevmseyhleSCIDtQTINHSQLKELPLILPSQRHGLRLLLEQKIHQLKVAYEIDGlhlLMESISQLE 236
Cdd:PRK11233 160 PLLKEDLFLVGTQ---------DCPG-QSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIG---EIESIATLT 226

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 375137193 237 MA-------TIQPAGA--SLNSRQDLCLLRVVEPAIErinylISLS-----EEELSPATLATKVVIRACVTNLINEKR 300
Cdd:PRK11233 227 AAiasgmgvTVLPESAarSLCGAVNGWMARITTPSMS-----LSLSlnlsaRLPLSPQAQAVKEILLSLVSSPVMEKR 299
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 90-283 1.14e-24

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: 98.44  E-value: 1.14e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPK 169
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 170 EvmseyHLESCIDTQTINhsQLKELPLILPSQRHGLRLLLE----QKIHQLKVAYEIDGLHLLMESISQLEMATIQPAGA 245
Cdd:cd05466   81 D-----HPLAKRKSVTLA--DLADEPLILFERGSGLRRLLDrafaEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESA 153

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 375137193 246 -SLNSRQDLCLLRVVEPAIERINYLISLSEEELSPATLA 283
Cdd:cd05466  154 vEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARA 192
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-265 7.25e-24

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 98.49  E-value: 7.25e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHS-SRLS-GHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPL 158
Cdd:PRK11242  81 AIHDvADLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 159 VKEQMFLispkeVMSEYH-LESCIDTQTInhSQLKELPLILPSQRHGLRLLLEQKIHQL----KVAYEIDGLHLLMESIS 233
Cdd:PRK11242 161 FTETLAL-----VVGRHHpLAARRKALTL--DELADEPLVLLSAEFATREQIDRYFRRHgvtpRVAIEANSISAVLEIVR 233

                        250       260       270
                 ....*....|....*....|....*....|..
gi 375137193 234 QLEMATIQPAgASLNSRQDLCLLRVVEPAIER 265
Cdd:PRK11242 234 RGRLATLLPA-AIAREHDGLCAIPLDPPLPQR 264
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-289 4.57e-23

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: 96.53  E-value: 4.57e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQ--LALRH-LDH 77
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKemLDLWEkLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  78 AVDSaHSSRLSGHVTVGFSpsvaAVIGTHFL----KLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQW 153
Cdd:NF040786  81 EFDR-YGKESKGVLRIGAS----TIPGQYLLpellKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 154 AIQPLVKEQMFLISPKEvMSEYHlescIDTQTINHSQLKELPLILPSQRHGLRLLLEQKIH-------QLKVAYEIDGLH 226
Cdd:NF040786 156 VYTPFYKDRLVLITPNG-TEKYR----MLKEEISISELQKEPFIMREEGSGTRKEAEKALKslgisleDLNVVASLGSTE 230

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375137193 227 LLMES---------ISQLematiqpAGASLNSRQDLCLLRVVEPAIERINYLISLSEEELSPATLATKVVIR 289
Cdd:NF040786 231 AIKQSveaglgisvISEL-------AAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-283 1.34e-21

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 90.43  E-value: 1.34e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   88 SGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLIS 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  168 PKevmsEYHLEsciDTQTINHSQLKELPLILPSQRHGLRLLLEQKIHQ----LKVAYEIDGLHLLMESISQLEMATIQPA 243
Cdd:pfam03466  81 PP----DHPLA---RGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAaglrPRVVLEVNSLEALLQLVAAGLGIALLPR 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 375137193  244 GASLNSRQD--LCLLRVVEPAIERINYLISLSEEELSPATLA 283
Cdd:pfam03466 154 SAVARELADgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRA 195
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-283 4.28e-18

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: 80.65  E-value: 4.28e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPK 169
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 170 EvmseyHleSCIDTQTINHSQLKELPLILPSQRHGLRLLLEQKIHQ----LKVAYEIDGLHllmesiSQLEMA------T 239
Cdd:cd08440   81 D-----H--PLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAagltLRPAYEVSHMS------TALGMVaaglgvA 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 375137193 240 IQPAGASLN-SRQDLCLLRVVEPAIERINYLISLSEEELSPATLA 283
Cdd:cd08440  148 VLPALALPLaDHPGLVARPLTEPVVTRTVGLIRRRGRSLSPAAQA 192
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-159 1.18e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 81.35  E-value: 1.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHS-SRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLS-GDLKALVNArQLDVAI----IFSDDVDPQWA 154
Cdd:PRK09906  81 RARKiVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITtQQEEKLRRG-ELDVGFmrhpVYSDEIDYLEL 159


                 ....*.
gi 375137193 155 I-QPLV 159
Cdd:PRK09906 160 LdEPLV 165
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.82e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.96  E-value: 3.82e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 375137193    3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10341 PRK10341
transcriptional regulator TdcA;
4-199 7.40e-15

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 73.74  E-value: 7.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   4 KQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVDSAH 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  84 SsrLSGHVTVGFSPSVAAVIGTHFLKLMRNR----YPDIKVRLIEGLSGDLKALVNARQLDVAI-IFSDDVDPQ-WAIQP 157
Cdd:PRK10341  90 G--MSSEAVVDVSFGFPSLIGFTFMSDMINKfkevFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgTLSNEMKLQdLHVEP 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 375137193 158 LVKEQMFLISPKevmseyhLESCidTQTINHSQLKELPLILP 199
Cdd:PRK10341 168 LFESEFVLVASK-------SRTC--TGTTTLESLKNEQWVLP 200
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 90-280 4.48e-14

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong 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: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 69.49  E-value: 4.48e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSvaavIGTHFLKLM----RNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFL 165
Cdd:cd08434    1 TVRLGFLHS----LGTSLVPDLirafRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 166 ISPKevmsEYHLESCidtQTINHSQLKELPLILPSQRHGLRL----LLEQKIHQLKVAYEIDGLHllmeSISQLEMA--- 238
Cdd:cd08434   77 VVPK----DHPLAGR---DSVDLAELADEPFVLLSPGFGLRPivdeLCAAAGFTPKIAFEGEEDS----TIAGLVAAglg 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 375137193 239 -TIQPAGASLNSRqDLCLLRVVEPAIERINYLISLSEEELSPA 280
Cdd:cd08434  146 vAILPEMTLLNPP-GVKKIPIKDPDAERTIGLAWLKDRYLSPA 187
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-163 3.32e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 68.88  E-value: 3.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVDSA 82
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  83 HSSRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLiegLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQ 162
Cdd:PRK10086  96 KNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI---LTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEE 172


                 .
gi 375137193 163 M 163
Cdd:PRK10086 173 I 173
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-170 1.54e-12

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 66.98  E-value: 1.54e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHL----D 76
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlkE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  77 HAvdSAHSSRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQ 156
Cdd:PRK11151  81 MA--SQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEV 158

                        170
                 ....*....|....
gi 375137193 157 PLVKEQMFLISPKE 170
Cdd:PRK11151 159 PLFDEPMLLAVYED 172
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-169 7.47e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 64.86  E-value: 7.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  17 SLGKAAKNLDIGTSALSQQISKLESELSIRLLQR----TALgtipTPAGLAFFQQVQLALRHLDHAVDSAHSSRLSGHVT 92
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRrnrsLLL----TEEGQRYFLDIREIFDQLAEATRKLRARSAKGALT 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  93 VGFSPSVAAvigtHFL--KLMR--NRYPDIKVRL-----IEGLSGDlkalvnarQLDVAIIFSDDVDPQWAIQPLVKEQM 163
Cdd:PRK11139  98 VSLLPSFAI----QWLvpRLSSfnEAHPDIDVRLkavdrLEDFLRD--------DVDVAIRYGRGNWPGLRVEKLLDEYL 165


                 ....*..
gi 375137193 164 F-LISPK 169
Cdd:PRK11139 166 LpVCSPA 172
PRK09791 PRK09791
LysR family transcriptional regulator;
1-125 1.41e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.01  E-value: 1.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 375137193  81 SAHS--SRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEG 125
Cdd:PRK09791  85 DIRQrqGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEG 131
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 90-283 5.88e-11

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: 60.60  E-value: 5.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLispk 169
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVV---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 170 eVMSEYHLESciDTQTINHSQLKELPLILPSQRHG------LRLLLEQKIHQLKVAYEIDGLHLLMESISQLEMATIQPA 243
Cdd:cd08414   77 -ALPADHPLA--ARESVSLADLADEPFVLFPREPGpglydqILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 375137193 244 GASLNSRQDLCLLRVVEPAIeRINYLISLSEEELSPATLA 283
Cdd:cd08414  154 SVARLQRPGVVYRPLADPPP-RSELALAWRRDNASPALRA 192
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-113 8.94e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 61.53  E-value: 8.94e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   4 KQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTiPTPAGLAFFQQVQlALRHLDHAVDSAH 83
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCR-PTPAGQRLLRHLR-QVALLEADLLSTL 82

                         90       100       110
                 ....*....|....*....|....*....|....
gi 375137193  84 SSRLSGHVTVgfspsVAAV----IGTHFLKLMRN 113
Cdd:PRK13348  83 PAERGSPPTL-----AIAVnadsLATWFLPALAA 111
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-143 1.17e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 61.31  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 ME-LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQqvqlALRHLDHAV 79
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQ----GCRRMLHEV 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375137193  80 DSAH------SSRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSG-DLKalvnARQLDVAI 143
Cdd:PRK10632  77 QDVHeqlyafNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPApDLI----ADGLDVVI 143
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-169 2.19e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.42  E-value: 2.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQ--LAL-RHLDHAV 79
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNriLALcEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  80 DSAHSSRlSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAII---FSDDVDPQWAIQ 156
Cdd:CHL00180  87 EDLKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggeVPTELKKILEIT 165

                        170
                 ....*....|...
gi 375137193 157 PLVKEQMFLISPK 169
Cdd:CHL00180 166 PYVEDELALIIPK 178
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-122 6.42e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 59.23  E-value: 6.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 375137193  81 SAHSSRLSGHVTVGFSPSVAAV---IGTHFLKLMRnRYPDIKVRL 122
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLhvhIGPMLAKFMA-RYPDVSLQL 125
PRK09986 PRK09986
LysR family transcriptional regulator;
3-180 1.53e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 57.81  E-value: 1.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVDSA 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  83 H--SSRLSGHVTVGfspsvaaVIGTHFLKLMRNR-------YPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQW 153
Cdd:PRK09986  89 EqiGRGEAGRIEIG-------IVGTALWGRLRPAmrhflkeNPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNP 161

                        170       180
                 ....*....|....*....|....*...
gi 375137193 154 AIQPL-VKEQMFLIspkeVMSEYHLESC 180
Cdd:PRK09986 162 GFTSRrLHESAFAV----AVPEEHPLAS 185
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 90-198 2.56e-09

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 56.03  E-value: 2.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPK 169
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100
                 ....*....|....*....|....*....
gi 375137193 170 EvmSEYHLESCIDTQtinhsQLKELPLIL 198
Cdd:cd08438   81 G--HPLAGRKTVSLA-----DLADEPFIL 102
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-283 4.79e-09

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: 55.30  E-value: 4.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDP-QWAIQPLVKEQMFLIsp 168
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPpGLASRELAREPLVAV-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 169 keVMSEYHLESCidtQTINHSQLKELPLI-LPSQrHGLRLLLEQKI--HQLK--VAYEIDGLHLLMESISQ-LEMAtIQP 242
Cdd:cd08436   79 --VAPDHPLAGR---RRVALADLADEPFVdFPPG-TGARRQVDRAFaaAGVRrrVAFEVSDVDLLLDLVARgLGVA-LLP 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 375137193 243 AGASLNsRQDLCLLRvVEPAIERINYLISlSEEELSPATLA 283
Cdd:cd08436  152 ASVAAR-LPGLAALP-LEPAPRRRLYLAW-SAPPPSPAARA 189
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-170 5.10e-09

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: 54.89  E-value: 5.10e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375137193 108 LKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIfsddVDPQWAI------QPLVKEQMFLISPKE 170
Cdd:cd08427   19 LARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIV----VEPPFPLpkdlvwTPLVREPLVLIAPAE 83
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 103-280 1.14e-08

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: 54.03  E-value: 1.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 103 IGTHFL----KLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISPKEvmseyHLE 178
Cdd:cd08420   10 IGEYLLprllARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD-----HPL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 179 SCIDTQTInhSQLKELPLILPSQRHGLRLLLEQKIHQLKVAyeIDGLHLLME--SISQLEMATIQPAGASLNSR------ 250
Cdd:cd08420   85 AGRKEVTA--EELAAEPWILREPGSGTREVFERALAEAGLD--GLDLNIVMElgSTEAIKEAVEAGLGISILSRlavrke 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 375137193 251 ---QDLCLLRVVEPAIERINYLISLSEEELSPA 280
Cdd:cd08420  161 lelGRLVALPVEGLRLTRPFSLIYHKDKYLSPA 193
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-205 1.27e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 52.33  E-value: 1.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  81 SAHSSRLSgHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDvaIIFSDDVDPQWAIQplvK 160
Cdd:PRK15421  82 ACNEPQQT-RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELD--LVMTSDILPRSGLH---Y 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 375137193 161 EQMFLISPKEVMSEYHlESCIDTQTINHSQLKELPLILPSQRHGL 205
Cdd:PRK15421 156 SPMFDYEVRLVLAPDH-PLAAKTRITPEDLASETLLIYPVQRSRL 199
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-80 2.19e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 51.31  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTAlGTIPTPAG---LAFFQQVQL----ALR 73
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGqrlLRHARQVRLleaeLLG 80


                 ....*..
gi 375137193  74 HLDHAVD 80
Cdd:PRK03635  81 ELPALDG 87
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-283 3.04e-07

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 49.90  E-value: 3.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWA-----IQPLVKEQMF 164
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDdpgltRVPLLDDPLD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 165 LISPKEvmseyHleSCIDTQTINHSQLKELPLILPSQRH----GLRLLLEQKIHQLKVAYEIDGLHllmesiSQLEM--- 237
Cdd:cd08423   81 LVLPAD-----H--PLAGREEVALADLADEPWIAGCPGSpchrWLVRACRAAGFTPRIAHEADDYA------TVLALvaa 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 375137193 238 ---ATIQPAGASLNSRQDLCLLRVVEPAIERInYLISLSEEELSPATLA 283
Cdd:cd08423  148 glgVALVPRLALGARPPGVVVRPLRPPPTRRI-YAAVRAGAARRPAVAA 195
PRK09801 PRK09801
LysR family transcriptional regulator;
4-175 4.88e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.42  E-value: 4.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   4 KQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVDSAH 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  84 S--SRLSGHVTVGFSPSVA-AVIGTHFLKLMRNrYPDIKVRLiEGLSGDLKALVNARQLDVAIifSDDVDPQWAIQPLVK 160
Cdd:PRK09801  89 QikTRPEGMIRIGCSFGFGrSHIAPAITELMRN-YPELQVHF-ELFDRQIDLVQDNIDLDIRI--NDEIPDYYIAHLLTK 164

                        170
                 ....*....|....*
gi 375137193 161 EQMFLISPKEVMSEY 175
Cdd:PRK09801 165 NKRILCAAPEYLQKY 179
PRK12680 PRK12680
LysR family transcriptional regulator;
1-169 1.56e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 48.85  E-value: 1.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESG-SLGKAAKNLDIGTSALSQQISKLESELSIRLLQRT--ALGTIpTPAGLAFFQQVQLALRHLDH 77
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKgrSLESV-TPAGVEVIERARAVLSEANN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  78 AVDSAHSSRL--SGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAI 155
Cdd:PRK12680  80 IRTYAANQRResQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI 159

                        170
                 ....*....|....*
gi 375137193 156 Q-PLVKEQMFLISPK 169
Cdd:PRK12680 160 AvPLYRWRRLVVVPR 174
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 89-206 3.59e-06

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: 46.75  E-value: 3.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  89 GHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLISP 168
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 375137193 169 KEvmseyHLESciDTQTINHSQLKELPLILPSQRHGLR 206
Cdd:cd08411   81 KD-----HPLA--KRKSVTPEDLAGERLLLLEEGHCLR 111
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-77 1.24e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 45.95  E-value: 1.24e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375137193   6 LKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDH 77
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLES 78
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 89-265 1.29e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 45.01  E-value: 1.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  89 GHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPLVKEQMFLisp 168
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLAL--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193 169 keVMSEYHLEScIDTQTINHSQLKELPLILPS-----QRHGLRLLLEQKIHQlKVAYEIDGLHLLMESISQLEMATIQPA 243
Cdd:cd08425   78 --VVGATHPLA-QRRTALTLDDLAAEPLALLSpdfatRQHIDRYFQKQGIKP-RIAIEANSISAVLEVVRRGRLATILPD 153

                        170       180
                 ....*....|....*....|..
gi 375137193 244 gASLNSRQDLCLLRVVEPAIER 265
Cdd:cd08425  154 -AIAREQPGLCAVALEPPLPGR 174
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-205 1.48e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 45.58  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  30 SALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRH---LDHAVDsAHSSRLSGH------VTVGFS--PS 98
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQwqqLRHTLD-QQGPSLSGElslfcsVTAAYShlPP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  99 VaavigthfLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAII-----FSDDVdpqwAIQPLVKEQMFLISPKevms 173
Cdd:PRK11716  85 I--------LDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAakpetLPASV----AFSPIDEIPLVLIAPA---- 148

                        170       180       190
                 ....*....|....*....|....*....|....
gi 375137193 174 eyhlESCIDTQTINHSQL--KELPLILPsqRHGL 205
Cdd:PRK11716 149 ----LPCPVRQQLSQEKPdwSRIPFILP--EHGP 176
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-143 2.85e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 44.97  E-value: 2.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESG-SLGKAAKNLDIGTSALSQQISKLESELSIRLLQR-----TALgtipTPAGLAFFQQVQLALRH 74
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhgkrlRGL----TEPGRIILASVERILQE 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375137193  75 LDH--AVDSAHSSRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAI 143
Cdd:PRK12684  77 VENlkRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 90-169 3.99e-05

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 43.80  E-value: 3.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  90 HVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAI-IFSDDVDPQ-WAIQPLVKEQMFLIS 167
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgRLADDEQPPdLASEELADEPLVVVA 80


                 ..
gi 375137193 168 PK 169
Cdd:cd08435   81 RP 82
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 95-198 5.85e-05

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 43.32  E-value: 5.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  95 FSPSVAAVIGthflkLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQ-WAIQPLVKEQMFLISPKEvms 173
Cdd:cd08451   12 FHPLVPGLIR-----RFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDgLVLELLLEEPMLVALPAG--- 83

                         90       100
                 ....*....|....*....|....*
gi 375137193 174 eyHleSCIDTQTINHSQLKELPLIL 198
Cdd:cd08451   84 --H--PLARERSIPLAALADEPFIL 104
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-144 1.49e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 42.75  E-value: 1.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTAL-------GTIPTPAGLAFFQQ---VQLAL 72
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKrlvvnehGRLLYPRALALLEQaveIEQLF 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375137193  73 RHLDHAVDSAHSSrlsghvtvgfspsvaaVIGTHFLKLM----RNRYPDIKVRLIEGLSGDLKALVNARQLDVAII 144
Cdd:PRK10837  85 REDNGALRIYASS----------------TIGNYILPAMiaryRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLI 144
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-69 2.94e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 41.96  E-value: 2.94e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375137193   4 KQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQ 69
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVK 72
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 98-211 6.44e-04

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


Pssm-ID: 176121  Cd Length: 199  Bit Score: 40.26  E-value: 6.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193  98 SVAAV--IGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAII-FSDDVDPQWAIQPLVKEQMFLISPKevmse 174
Cdd:cd08430    7 SVTASysFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAaRPDKLPARLAFLPLATSPLVFIAPN----- 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 375137193 175 yhlESCIDTQTINHSQL--KELPLILPSqrHGL-RLLLEQ 211
Cdd:cd08430   82 ---IACAVTQQLSQGEIdwSRLPFILPE--RGLaRERLDQ 116
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-86 1.25e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 39.98  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   3 LKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVDSA 82
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAA 85


                 ....
gi 375137193  83 HSSR 86
Cdd:PRK11013  86 ESLR 89
PRK11482 PRK11482
DNA-binding transcriptional regulator;
1-123 1.55e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 39.71  E-value: 1.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK11482  29 IDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGALD 108

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 375137193  81 SAHSSRLSGHVTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLI 123
Cdd:PRK11482 109 ITGSYDKQRTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI 151
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 91-158 1.58e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 39.06  E-value: 1.58e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 375137193  91 VTVGFSPSVAAVIGTHFLKLMRNRYPDIKVRLIEGLSGDLKALVNARQLDVAIIFSDDVDPQWAIQPL 158
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPL 69
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-121 8.99e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 37.32  E-value: 8.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375137193   1 MELKQLKYFIAVIESGSLGKAAKNLDIGTSALSQQISKLESELSIRLLQRTALGTIPTPAGLAFFQQVQLALRHLDHAVD 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 375137193  81 SAHSSRLSGHVTVGFSPSVAAVIgthfLKLMRNR----YP----DIKVR 121
Cdd:PRK15092  91 SLMYSNLQGVLTIGASDDTADTI----LPFLLNRvssvYPklalDVRVK 135
 
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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