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Conserved domains on  [gi|446345508|ref|WP_000423363|]
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MULTISPECIES: tricarballylate utilization LysR family transcriptional regulator TcuR [Salmonella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

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

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
90-287 2.48e-55

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: 178.17  E-value: 2.48e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIGsH 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVG-P 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 170 ALLAALPDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAI-SHLD 248
Cdd:cd08433   80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVaAEVA 159
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446345508 249 NDALRVIGVHNPVLSRPNFLVSLSDDELTPAGLAARVVL 287
Cdd:cd08433  160 AGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.01e-17

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 3.01e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446345508    3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAG 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) ...
90-287 2.48e-55

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: 178.17  E-value: 2.48e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIGsH 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVG-P 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 170 ALLAALPDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAI-SHLD 248
Cdd:cd08433   80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVaAEVA 159
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446345508 249 NDALRVIGVHNPVLSRPNFLVSLSDDELTPAGLAARVVL 287
Cdd:cd08433  160 AGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
1-272 4.96e-50

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 167.94  E-value: 4.96e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREA--RLSGHVSVGMAPST-ASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARP 157
Cdd:PRK11233  81 AVHNVgqALSGQVSIGLAPGTaASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 158 ILEEQLFLIGSHallaALPDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGAT 237
Cdd:PRK11233 161 LLKEDLFLVGTQ----DCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVT 236
                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 446345508 238 LQPGAAishldndALRVIGVHNPVLSR---PNFLVSLS 272
Cdd:PRK11233 237 VLPESA-------ARSLCGAVNGWMARittPSMSLSLS 267
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 3.06e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.56  E-value: 3.06e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREAR--LSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPI 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 159 LEEQLFLIGShallaalPDNPitpeqLAGIPLIMPSqghglrgrldavcqehalnveivaeidgLALLMRAVRDGLGATL 238
Cdd:COG0583  161 GEERLVLVAS-------PDHP-----LARRAPLVNS----------------------------LEALLAAVAAGLGIAL 200
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446345508 239 QPG-AAISHLDNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:COG0583  201 LPRfLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPA 242
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
88-279 3.25e-27

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: 105.45  E-value: 3.25e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   88 SGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIG 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  168 S--HALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAIS 245
Cdd:pfam03466  81 PpdHPLARG---EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 446345508  246 H-LDNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:pfam03466 158 ReLADGRLVALPLPEPPLPRELYLVWRKGRPLSPA 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.01e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 3.01e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446345508    3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-65 3.63e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 62.86  E-value: 3.63e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446345508   1 ME-LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFY 65
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYY 66
 
Name Accession Description Interval E-value
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
90-287 2.48e-55

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: 178.17  E-value: 2.48e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIGsH 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVG-P 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 170 ALLAALPDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAI-SHLD 248
Cdd:cd08433   80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVaAEVA 159
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446345508 249 NDALRVIGVHNPVLSRPNFLVSLSDDELTPAGLAARVVL 287
Cdd:cd08433  160 AGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
1-272 4.96e-50

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 167.94  E-value: 4.96e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREA--RLSGHVSVGMAPST-ASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARP 157
Cdd:PRK11233  81 AVHNVgqALSGQVSIGLAPGTaASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 158 ILEEQLFLIGSHallaALPDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGAT 237
Cdd:PRK11233 161 LLKEDLFLVGTQ----DCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVT 236
                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 446345508 238 LQPGAAishldndALRVIGVHNPVLSR---PNFLVSLS 272
Cdd:PRK11233 237 VLPESA-------ARSLCGAVNGWMARittPSMSLSLS 267
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 3.06e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.56  E-value: 3.06e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREAR--LSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPI 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 159 LEEQLFLIGShallaalPDNPitpeqLAGIPLIMPSqghglrgrldavcqehalnveivaeidgLALLMRAVRDGLGATL 238
Cdd:COG0583  161 GEERLVLVAS-------PDHP-----LARRAPLVNS----------------------------LEALLAAVAAGLGIAL 200
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446345508 239 QPG-AAISHLDNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:COG0583  201 LPRfLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPA 242
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
1-264 7.30e-31

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 117.36  E-value: 7.30e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREAR-LS-GHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPI 158
Cdd:PRK11242  81 AIHDVAdLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 159 LEEQLFLIGSHALLAALPDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATL 238
Cdd:PRK11242 161 FTETLALVVGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATL 240
                        250       260
                 ....*....|....*....|....*.
gi 446345508 239 QPgAAISHlDNDALRVIGVHNPVLSR 264
Cdd:PRK11242 241 LP-AAIAR-EHDGLCAIPLDPPLPQR 264
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
90-279 2.18e-29

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: 110.77  E-value: 2.18e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIGS- 168
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPp 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 169 -HALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAISHL 247
Cdd:cd05466   81 dHPLAKR---KSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157
                        170       180       190
                 ....*....|....*....|....*....|..
gi 446345508 248 DNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPA 189
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
88-279 3.25e-27

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: 105.45  E-value: 3.25e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   88 SGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIG 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  168 S--HALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAIS 245
Cdd:pfam03466  81 PpdHPLARG---EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 446345508  246 H-LDNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:pfam03466 158 ReLADGRLVALPLPEPPLPRELYLVWRKGRPLSPA 192
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-279 5.57e-21

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: 88.35  E-value: 5.57e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIG-- 167
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCpk 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 168 SHALlAALPdnPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAISHL 247
Cdd:cd08440   81 DHPL-ARRR--SVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLA 157
                        170       180       190
                 ....*....|....*....|....*....|..
gi 446345508 248 DNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:cd08440  158 DHPGLVARPLTEPVVTRTVGLIRRRGRSLSPA 189
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
1-293 7.31e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 87.52  E-value: 7.31e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREARLSGHV-SVGMAPStASILGIPFIHAMqenyadVRLHVVESLSgNLERMINTRQI------DLAIVFQKDKIlrw 153
Cdd:PRK09906  81 RARKIVQEDRQlTIGFVPS-AEVNLLPKVLPM------FRLRHPDTLI-ELVSLITTQQEeklrrgELDVGFMRHPV--- 149
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 154 sARPILEEQLFLigSHALLAALPDN-------PITPEQLAGIPLIMPS--QGHGLRGRLDAVCQEHALNVEIVAEIDGLA 224
Cdd:PRK09906 150 -YSDEIDYLELL--DEPLVVVLPVDhplahekEITAAQLDGVNFISTDpaYSGSLAPIIKAWFAQHNSQPNIVQVATNIL 226
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 225 LLMRAVRDGLGATLQPGAAISHL-DNDALRVIGVHNPVLsrpNFLVSLSDDELTPAGLAARVVLTKVMRQ 293
Cdd:PRK09906 227 VTMNLVGMGLGCTIIPGYMNNFNtGQVVFRPLAGNVPSI---ALLMAWKKGEMKPALRDFIAIVQERLAS 293
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.01e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 3.01e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446345508    3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
21-145 5.31e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 73.88  E-value: 5.31e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  21 AAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAILAAREARLSGHVSVGMAPSTA 100
Cdd:PRK10086  34 AADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELSGTLTVYSRPSIA 113
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446345508 101 SILGIPFIHAMQENYADVRLHVvesLSGNLERMINTRQIDLAIVF 145
Cdd:PRK10086 114 QCWLVPRLADFTRRYPSISLTI---LTGNENVNFQRAGIDLAIYF 155
PRK09791 PRK09791
LysR family transcriptional regulator;
1-141 7.42e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 70.56  E-value: 7.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQL---ALRHADD 77
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLileELRAAQE 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446345508  78 AILaAREARLSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVEslsGNLERMINT-RQIDL 141
Cdd:PRK09791  85 DIR-QRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME---GQLVSMINElRQGEL 145
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
90-263 3.17e-13

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: 67.20  E-value: 3.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQkdkilrwsarPILEEQL--FLIG 167
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVL----------PVDEEEFdsQPLC 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 168 SHALLAALPDN-------PITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQP 240
Cdd:cd08438   71 NEPLVAVLPRGhplagrkTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLP 150
                        170       180
                 ....*....|....*....|...
gi 446345508 241 GAAISHLDNDALRVIGVHNPVLS 263
Cdd:cd08438  151 RSIAQRLDNAGVKVIPLTDPDLR 173
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
1-264 6.39e-13

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 67.75  E-value: 6.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHA----D 76
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlkE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  77 DAILAAREarLSGHVSVGMAPSTASILgIPFI-HAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSA 155
Cdd:PRK11151  81 MASQQGET--MSGPLHIGLIPTVGPYL-LPHIiPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 156 RPILEEQLfligshaLLAALPDNP------ITPEQLAGIPLIMPSQGHGLRGRLDAVC-------QEH--ALNVEIvaei 220
Cdd:PRK11151 158 VPLFDEPM-------LLAVYEDHPwanrdrVPMSDLAGEKLLMLEDGHCLRDQAMGFCfeagadeDTHfrATSLET---- 226
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 446345508 221 dglalLMRAVRDGLGATLQPG-AAISHLDNDALRVIGVHNPVLSR 264
Cdd:PRK11151 227 -----LRNMVAAGSGITLLPAlAVPNERKRDGVCYLPCIKPEPRR 266
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
89-264 1.93e-12

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: 65.04  E-value: 1.93e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  89 GHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLI-G 167
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVvG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 168 SHALLAALPDnPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPgAAISHl 247
Cdd:cd08425   81 ATHPLAQRRT-ALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILP-DAIAR- 157
                        170
                 ....*....|....*..
gi 446345508 248 DNDALRVIGVHNPVLSR 264
Cdd:cd08425  158 EQPGLCAVALEPPLPGR 174
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
106-279 3.49e-12

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: 64.05  E-value: 3.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 106 PFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIV---FQKDKIlrwSARPILEEQLFLIGS--HALLAalpDNPI 180
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVegpVDHPDL---IVEPFAEDELVLVVPpdHPLAG---RKEV 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 181 TPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVE---IVAEIDGLALLMRAVRDGLGATLQPGAAISH-LDNDALRVIG 256
Cdd:cd08420   91 TAEELAAEPWILREPGSGTREVFERALAEAGLDGLdlnIVMELGSTEAIKEAVEAGLGISILSRLAVRKeLELGRLVALP 170
                        170       180
                 ....*....|....*....|...
gi 446345508 257 VHNPVLSRPNFLVSLSDDELTPA 279
Cdd:cd08420  171 VEGLRLTRPFSLIYHKDKYLSPA 193
PRK10341 PRK10341
transcriptional regulator TdcA;
4-257 1.26e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 64.11  E-value: 1.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   4 RQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAILAAR 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  84 eaRLSGHVSVGMAPSTASILGIPF----IHAMQENYADVRLHVVESLSGNLERMINTRQIDLAI--VFQKDKILRWSARP 157
Cdd:PRK10341  90 --GMSSEAVVDVSFGFPSLIGFTFmsdmINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEP 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 158 ILEEQLFLIGSHALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGAT 237
Cdd:PRK10341 168 LFESEFVLVASKSRTCT---GTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLT 244
                        250       260
                 ....*....|....*....|
gi 446345508 238 LQPGAAISHLDNDALRVIGV 257
Cdd:PRK10341 245 VIPCDMTSPFGSNQFITIPI 264
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
90-243 3.29e-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: 61.37  E-value: 3.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLI--G 167
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVAlpA 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446345508 168 SHALLAAlpdNPITPEQLAGIPLIMPSQGH--GLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAA 243
Cdd:cd08414   81 DHPLAAR---ESVSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASV 155
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-65 3.63e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 62.86  E-value: 3.63e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446345508   1 ME-LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFY 65
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYY 66
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-290 3.94e-11

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: 61.08  E-value: 3.94e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVfqkdkilRWSARPILEEQLFLIGSH 169
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFV-------GLPERRPPGLASRELARE 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 170 ALLAAL-PDNP------ITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGA 242
Cdd:cd08436   74 PLVAVVaPDHPlagrrrVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPAS 153
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 446345508 243 AISHLdnDALRVIGVHnPVLSRPNFLVSLSDdeltPAGLAARVVLTKV 290
Cdd:cd08436  154 VAARL--PGLAALPLE-PAPRRRLYLAWSAP----PPSPAARAFLELL 194
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
21-191 4.41e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 62.55  E-value: 4.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  21 AAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQ---LALRHADDAILaAREARlsGHVSVGMAP 97
Cdd:PRK11139  26 AAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIReifDQLAEATRKLR-ARSAK--GALTVSLLP 102
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  98 STASILGIPFIHAMQENYA--DVRLHVVESLSGNLerminTRQIDLAIVFQKDKILRWSARPILEEQLFLIGSHALLAAl 175
Cdd:PRK11139 103 SFAIQWLVPRLSSFNEAHPdiDVRLKAVDRLEDFL-----RDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALLNG- 176
                        170
                 ....*....|....*..
gi 446345508 176 pDNPI-TPEQLAGIPLI 191
Cdd:PRK11139 177 -GKPLkTPEDLARHTLL 192
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
89-264 4.88e-11

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: 61.00  E-value: 4.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  89 GHVSVGMAPSTASILgIP-FIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVfqkdkilrwsARPILEEQL--FL 165
Cdd:cd08411    1 GPLRLGVIPTIAPYL-LPrLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALL----------ALPVDEPGLeeEP 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 166 IGSHALLAALPDN-------PITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATL 238
Cdd:cd08411   70 LFDEPFLLAVPKDhplakrkSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITL 149
                        170       180
                 ....*....|....*....|....*...
gi 446345508 239 QPGAAI--SHLDNDALRVIGVHNPVLSR 264
Cdd:cd08411  150 LPELAVpsEELRGDRLVVRPFAEPAPSR 177
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
1-203 1.83e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 60.77  E-value: 1.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDA-- 78
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAqd 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  79 ILAAREARLSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESlsgNLERMINTRQIDLAIvfqkdkilRWSARPI 158
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEAT---NRRVDVVGEGVDVAI--------RVRPRPF 150
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446345508 159 LEEQLF----------LIGSHALLAALpDNPITPEQLAGIP-LIMPSQGHGLRGRL 203
Cdd:PRK14997 151 EDSDLVmrvladrghrLFASPDLIARM-GIPSAPAELSHWPgLSLASGKHIHRWEL 205
PRK09986 PRK09986
LysR family transcriptional regulator;
3-240 3.52e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 59.74  E-value: 3.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAI--- 79
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLarv 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  80 --LAAREArlsGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIvfqkdkilrW-SAR 156
Cdd:PRK09986  89 eqIGRGEA---GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGI---------WrMAD 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 157 PILEEQL--FLIGSHALLAALP-DNP------ITPEQLAGIPLI-MPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALL 226
Cdd:PRK09986 157 LEPNPGFtsRRLHESAFAVAVPeEHPlasrssVPLKALRNEYFItLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTV 236
                        250
                 ....*....|....
gi 446345508 227 MRAVRDGLGATLQP 240
Cdd:PRK09986 237 LAMVSMGIGITLLP 250
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
90-279 4.07e-10

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: 58.32  E-value: 4.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILgIP-FIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLI-- 166
Cdd:cd08434    1 TVRLGFLHSLGTSL-VPdLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVvp 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 167 GSHALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIV---AEIDGLALLMRAvrdGLGATLQPGAA 243
Cdd:cd08434   80 KDHPLAGR---DSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAfegEEDSTIAGLVAA---GLGVAILPEMT 153
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 446345508 244 IshLDNDALRVIGVHNPVLSRPNFLVSLSDDELTPA 279
Cdd:cd08434  154 L--LNPPGVKKIPIKDPDAERTIGLAWLKDRYLSPA 187
rbcR CHL00180
LysR transcriptional regulator; Provisional
3-245 9.48e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 58.49  E-value: 9.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAF--YSQAQLAL-RHADDAI 79
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLlrYGNRILALcEETCRAL 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  80 LAAREARlSGHVSVGMAPSTASILGIPFIHAMQENYA--DVRLHV--VESLSGNlermINTRQIDLAIV-----FQKDKI 150
Cdd:CHL00180  87 EDLKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPqiNVQLQVhsTRRIAWN----VANGQIDIAIVggevpTELKKI 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 151 LrwSARPILEEQLFLI--GSHAlLAALPDnpITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNV---EIVAEIDGLAL 225
Cdd:CHL00180 162 L--EITPYVEDELALIipKSHP-FAKLKK--IQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSkrfKIEMELNSIEA 236
                        250       260
                 ....*....|....*....|
gi 446345508 226 LMRAVRDGLGATLQPGAAIS 245
Cdd:CHL00180 237 IKNAVQSGLGAAFVSVSAIE 256
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-113 2.25e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.21  E-value: 2.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   4 RQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTsRGVTPTNAGLAFYSQA-QLALRHADdaILAA 82
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLrQVALLEAD--LLST 81
                         90       100       110
                 ....*....|....*....|....*....|.
gi 446345508  83 REARLSGHVSVGMAPSTASiLGIPFIHAMQE 113
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADS-LATWFLPALAA 111
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
3-269 2.36e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 54.31  E-value: 2.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAILAA 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  83 REArlSGHVSVGMAPSTASILGIPFIHAMQENYADVRLhvvESLSGNLERMINTR---QIDLAIVFQKDKILRWSARPIL 159
Cdd:PRK10837  85 RED--NGALRIYASSTIGNYILPAMIARYRRDYPQLPL---ELSVGNSQDVINAVldfRVDIGLIEGPCHSPELISEPWL 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 160 EEQL--FLIGSHALLAalpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGAT 237
Cdd:PRK10837 160 EDELvvFAAPDSPLAR----GPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGIS 235
                        250       260       270
                 ....*....|....*....|....*....|...
gi 446345508 238 -LQPGAAISHLDNDALRVIGVHNPVLSRPNFLV 269
Cdd:PRK10837 236 cLSRRVIADQLQAGTLVEVAVPLPRLMRTLYRI 268
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
1-143 4.48e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 53.49  E-value: 4.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345508  81 AAREARLSGHVSVGMAPSTASILgIPFI-HAMQENYADVRLHVVESLSGNLERMINTRQIDLAI 143
Cdd:PRK15092  91 SLMYSNLQGVLTIGASDDTADTI-LPFLlNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK09801 PRK09801
LysR family transcriptional regulator;
4-142 2.54e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 51.19  E-value: 2.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   4 RQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRH----ADDai 79
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQyqrlVDD-- 86
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446345508  80 LAAREARLSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVveslsgnlerMINTRQIDLA 142
Cdd:PRK09801  87 VTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF----------ELFDRQIDLV 139
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-264 1.22e-06

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: 47.95  E-value: 1.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIV----FQKDKILRWSarPILEEQLFL 165
Cdd:cd08427    1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVveppFPLPKDLVWT--PLVREPLVL 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 166 IGSHALLAALPdnpitPEQLAGIPLIMPSQgHGLRGRL-DAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAI 244
Cdd:cd08427   79 IAPAELAGDDP-----RELLATQPFIRYDR-SAWGGRLvDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAV 152
                        170       180
                 ....*....|....*....|
gi 446345508 245 SHLDNDALRVIGVHNPVLSR 264
Cdd:cd08427  153 PLPAGPRVRVLPLGDPAFSR 172
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
1-235 1.42e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 48.83  E-value: 1.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETG-SMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSR---GVTPtnAGLAFYSQAQLALRHAD 76
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKrlkGLTE--PGKAVLDVIERILREVG 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  77 DAILAARE--ARLSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQ---KDKIL 151
Cdd:PRK12682  79 NIKRIGDDfsNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATEslaDDPDL 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 152 ------RWSARPILEEqlfligSHALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLAL 225
Cdd:PRK12682 159 atlpcyDWQHAVIVPP------DHPLAQE---ERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDV 229
                        250
                 ....*....|
gi 446345508 226 LMRAVRDGLG 235
Cdd:PRK12682 230 IKTYVRLGLG 239
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
93-238 2.77e-06

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 47.17  E-value: 2.77e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  93 VGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQkdkilrwsarPILEEQLFL--IGSHA 170
Cdd:cd08415    4 IAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASL----------PLDHPGLESepLASGR 73
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446345508 171 LLAALPDN-------PITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATL 238
Cdd:cd08415   74 AVCVLPPGhplarkdVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAI 148
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-254 5.03e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 47.32  E-value: 5.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  81 AAREARLSgHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLaiVFQKDKI----LRWSAR 156
Cdd:PRK15421  82 ACNEPQQT-RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL--VMTSDILprsgLHYSPM 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 157 PILEEQLFLIGSHALLAalpDNPITPEQLAG-IPLIMPSQghglRGRLDAvcQEHALNVEIVA----EIDGLALLMRAVR 231
Cdd:PRK15421 159 FDYEVRLVLAPDHPLAA---KTRITPEDLASeTLLIYPVQ----RSRLDV--WRHFLQPAGVSpslkSVDNTLLLIQMVA 229
                        250       260
                 ....*....|....*....|...
gi 446345508 232 DGLGATLQPGAAISHLDNDALRV 254
Cdd:PRK15421 230 ARMGIAALPHWVVESFERQGLVV 252
PRK12680 PRK12680
LysR family transcriptional regulator;
1-144 1.61e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 45.77  E-value: 1.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIietgsmgsAAQDLDIGVSA---------LSQQMSRLENELAIRLLQRTSR---GVTPtnAGLAFYSQA 68
Cdd:PRK12680   1 MTLTQLRYLVAI--------ADAELNITLAAarvhatqpgLSKQLKQLEDELGFLLFVRKGRsleSVTP--AGVEVIERA 70
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446345508  69 QLALRHADDA-ILAAREARLS-GHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIV 144
Cdd:PRK12680  71 RAVLSEANNIrTYAANQRRESqGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIV 148
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-69 2.18e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 45.18  E-value: 2.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345508   6 LRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQ 69
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQAR 70
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
3-236 2.92e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 44.98  E-value: 2.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   3 LRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRHADDAILAA 82
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAA 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  83 ---REARlSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVfQKDKILRWSARPIL 159
Cdd:PRK11013  86 eslREFR-QGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLT-ETLHTPAGTERTEL 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 160 ---EEQLFLIGSHALLAalpDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGA 236
Cdd:PRK11013 164 ltlDEVCVLPAGHPLAA---KKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGV 240
cbl PRK12679
HTH-type transcriptional regulator Cbl;
30-217 3.22e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 44.80  E-value: 3.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  30 SALSQQMSRLENELAIRL-LQRTSRGVTPTNAGLAFYSQAQLALRHADD----AILAAREArlSGHVSVGMAPSTASILG 104
Cdd:PRK12679  31 SGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNvrrlADLFTNDT--SGVLTIATTHTQARYSL 108
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 105 IPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQkdkilRWSARPILEEQLFLIGSHALLaaLPDN------ 178
Cdd:PRK12679 109 PEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE-----RLSNDPQLVAFPWFRWHHSLL--VPHDhpltqi 181
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446345508 179 -PITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIV 217
Cdd:PRK12679 182 tPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIV 221
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
90-287 4.35e-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: 4.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAI-----VFQKDKIlrwSARPILEEQLF 164
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrladDEQPPDL---ASEELADEPLV 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 165 LI-GSHALLAALPdnPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNV-EIVAEIDGLALLMRAV-RDGLGATLQPG 241
Cdd:cd08435   78 VVaRPGHPLARRA--RLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALLaRSDMLAVLPRS 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 446345508 242 AAISHLDNDALRVIGVHNPVLSRPNFLVSLSDDELTPAGLAARVVL 287
Cdd:cd08435  156 VAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
90-274 5.06e-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: 5.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIP-FIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIV---FQKDKILRwsARPILEEQlfl 165
Cdd:cd08451    1 RLRVGFTSSAAFHPLVPgLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVrppVARSDGLV--LELLLEEP--- 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 166 igshaLLAALP-------DNPITPEQLAGIPLIM--PSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGA 236
Cdd:cd08451   76 -----MLVALPaghplarERSIPLAALADEPFILfpRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGV 150
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446345508 237 TLQPgAAISHLDNDALRVIGVHNPVLSRPNFLVSLSDD 274
Cdd:cd08451  151 SIVP-ASMRQLQAPGVVYRPLAGAPLTAPLALAYRRGE 187
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
172-247 5.47e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 43.45  E-value: 5.47e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446345508 172 LAALPdnPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAISHL 247
Cdd:cd08426   84 LARQP--SVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRRE 157
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
90-242 7.33e-05

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 42.95  E-value: 7.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSG-NLERmintRQIDLAIVFQKDkilRWS---ARPILEEQLFL 165
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLvDFAR----EGIDLAIRYGDG---DWPgleAERLMDEELVP 73
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446345508 166 IGSHALLAALPdnPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGA 242
Cdd:cd08432   74 VCSPALLAGLP--LLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRA 148
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
117-282 1.03e-04

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 42.49  E-value: 1.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 117 DVRLHVveslsGNLE---RMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIGS--HALLAAlpdNPITPEQLAGIPLI 191
Cdd:cd08419   29 EVSLRV-----GNREqvlERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPpdHPLAGQ---KRIPLERLAREPFL 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 192 MPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQPGAAISH-LDNDALRVIGV-HNPVLsRPNFLV 269
Cdd:cd08419  101 LREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALeLATGRLAVLDVeGFPIR-RQWYVV 179
                        170
                 ....*....|...
gi 446345508 270 SLSDDELTPAGLA 282
Cdd:cd08419  180 HRKGKRLSPAAQA 192
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-74 1.04e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 42.88  E-value: 1.04e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446345508  30 SALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQLALRH 74
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQ 50
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
92-238 1.52e-04

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 42.02  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  92 SVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKdkilrwSARPILEEQLFLigSHAL 171
Cdd:cd08456    3 RIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTL------HEPPGIERERLL--RIDG 74
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345508 172 LAALPDNP-------ITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATL 238
Cdd:cd08456   75 VCVLPPGHrlavkkvLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSV 148
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
1-217 2.20e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 42.34  E-value: 2.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETG-SMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTP-TNAGLAFYSQAQLALRHADDA 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGlTEPGKELLQIVERMLLDAENL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  79 ILAARE--ARLSGHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQK-DKILRWSA 155
Cdd:PRK12683  81 RRLAEQfaDRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAlDREPDLVS 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345508 156 RPILEEQLFLIGS--HALLAAlpdNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIV 217
Cdd:PRK12683 161 FPYYSWHHVVVVPkgHPLTGR---ENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIV 221
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
89-240 2.43e-04

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 41.27  E-value: 2.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  89 GHVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESlsgnlERMIN--TRQIDLAIVFQKDKILRWSARPILEEQLFLI 166
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLS-----DRLVDlvEEGFDLAIRIGELPDSSLVARRLGPVRRVLV 75
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446345508 167 GSHALLAALPdNPITPEQLAGIP-LIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQP 240
Cdd:cd08422   76 ASPAYLARHG-TPQTPEDLARHRcLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLP 149
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-283 2.79e-04

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 41.04  E-value: 2.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVF-------QKDKILRWsaRPILEEQ 162
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFdypvtppPDDPGLTR--VPLLDDP 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508 163 LFLI--GSHALLAALPdnpITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRDGLGATLQP 240
Cdd:cd08423   79 LDLVlpADHPLAGREE---VALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVP 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 446345508 241 GAAISHLdNDALRVIGVHnPVLSRPNFLVSLSDDELTPAGLAA 283
Cdd:cd08423  156 RLALGAR-PPGVVVRPLR-PPPTRRIYAAVRAGAARRPAVAAA 196
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-88 2.80e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 41.68  E-value: 2.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508   1 MELRQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTsRGVTPTNAG---LAFYSQAQLaLRH--- 74
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGqrlLRHARQVRL-LEAell 79
                         90
                 ....*....|....
gi 446345508  75 ADDAILAAREARLS 88
Cdd:PRK03635  80 GELPALDGTPLTLS 93
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
90-232 1.29e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 39.12  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345508  90 HVSVGMAPSTASILGIPFIHAMQENYADVRLHVVESLSGNLERMINTRQIDLAIVFQKDKILRWSARPILEEQLFLIGSH 169
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446345508 170 ALLAAlpDNPITPEQLAGIPLIMPSQGHGLRGRLDAVCQEHALNVEIVAEIDGLALLMRAVRD 232
Cdd:cd08417   81 DHPLA--GGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAG 141
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-69 2.04e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 39.27  E-value: 2.04e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446345508   4 RQLRYFVRIIETGSMGSAAQDLDIGVSALSQQMSRLENELAIRLLQRTSRGVTPTNAGLAFYSQAQ 69
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVK 72
 
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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