NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|495778556|ref|WP_008503135|]
View 

MULTISPECIES: DNA-binding transcriptional regulator YhaJ [Enterobacteriaceae]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 99-291 5.47e-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 cd08431:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 176.69  E-value: 5.47e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  99 LTLVTEALVPTEALFPLVDRLAAKAN-TQLSIITEVLAGAWERLETGRADIVIAPDmHFRSSSEINSRKLYSVMNVYVAA 177
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKaTRIRLSEEVLGGTWDALASGRADLVIGAT-GELPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 178 PNHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGR 257
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495778556 258 LrvVSPEY---TSEVDIIMAWRRDSMGEAKSWCLREI 291
Cdd:cd08431  161 L--VEKALedpRPPQELFLAWRKDQRGKALAWFVQRL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 2.75e-15

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.95  E-value: 2.75e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556    9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 99-291 5.47e-55

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 176.69  E-value: 5.47e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  99 LTLVTEALVPTEALFPLVDRLAAKAN-TQLSIITEVLAGAWERLETGRADIVIAPDmHFRSSSEINSRKLYSVMNVYVAA 177
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKaTRIRLSEEVLGGTWDALASGRADLVIGAT-GELPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 178 PNHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGR 257
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495778556 258 LrvVSPEY---TSEVDIIMAWRRDSMGEAKSWCLREI 291
Cdd:cd08431  161 L--VEKALedpRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-288 1.11e-46

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 158.95  E-value: 1.11e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEA 90
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  91 LARGWETHLTLVTEALVPTEALFPLV-DRLAAKANTQLSIITEVLAGAWERLETGRADIVI-----AP---DMHFRSSSE 161
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIvDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatraIPvggRFAFRDMGM 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 162 INSRklysvmnvYVAAPNHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGV 241
Cdd:PRK11074 166 LSWA--------CVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCV 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 495778556 242 ATMPYPFVEKDIAEGRL---RVVSPEYTSEVdiIMAWRRDSMGEAKSWCL 288
Cdd:PRK11074 238 GMVPTHFAKPLINSGKLvelTLENPFPDSPC--CLTWQQNDMSPALAWLL 285
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-278 2.98e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.77  E-value: 2.98e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTT 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  87 DAEALARGWETHLTLVTEALVPTEALFPLVDRLAAKA-NTQLSIITEVLAGAWERLETGRADIVIAPDMHfrSSSEINSR 165
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRLVDALLEGELDLAIRLGPP--PDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 166 KLYSVMNVYVAAPNHPIhqepeplsevtrvkyrgvavadtARERPVltvqlldkqprltVTSLEDKRQALLAGLGVATMP 245
Cdd:COG0583  159 PLGEERLVLVASPDHPL-----------------------ARRAPL-------------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270
                 ....*....|....*....|....*....|....
gi 495778556 246 YPFVEKDIAEGRLRVVS-PEYTSEVDIIMAWRRD 278
Cdd:COG0583  203 RFLAADELAAGRLVALPlPDPPPPRPLYLVWRRR 236
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 2.75e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.95  E-value: 2.75e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556    9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 98-279 6.39e-13

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: 66.16  E-value: 6.39e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   98 HLTLVTEALVPTEALFPLVDRLAAKA-NTQLSIITEVLAGAWERLETGRADIVIApdMHFRSSSEINSRKLYSVMNVYVA 176
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYpDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  177 APNHPIHQ-EPEPLSEVTRVKY--RGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDI 253
Cdd:pfam03466  81 PPDHPLARgEPVSLEDLADEPLilLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180
                  ....*....|....*....|....*..
gi 495778556  254 AEGRLRVVS-PEYTSEVDIIMAWRRDS 279
Cdd:pfam03466 161 ADGRLVALPlPEPPLPRELYLVWRKGR 187
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-94 3.36e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 59.65  E-value: 3.36e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   8 TLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERG-RV--LLEAADKL 84
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnRIlaLCEETCRA 85

                         90
                 ....*....|
gi 495778556  85 TTDAEALARG 94
Cdd:CHL00180  86 LEDLKNLQRG 95
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-279 1.31e-07

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 51.84  E-value: 1.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRsGHRTKFTNVGRMLLERGR--VLLEAadKLTTDA 88
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARqvRLLEA--ELLAEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   89 EALARGWETHLTLVTEALVPTEALFPLVDRLAAKANTQLSIITEVLAGAWERLETGRAdiVIAPDMHFRSSSEINSRKLY 168
Cdd:TIGR03298  82 PGLAPGAPTRLTIAVNADSLATWFLPALAPVLAREGVLLDLVVEDQDHTAELLRSGEV--LGAVTTEAKPVPGCRVVPLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  169 SVMNVYVAAPnhPIHQepeplsevtrvKY--RGVaVADTARERPVLT--------VQLLDKQ-------PRLTVTSLEDK 231
Cdd:TIGR03298 160 AMRYLAVASP--AFAA-----------RYfpDGV-TAAALARAPVIVfnrkddlqDRFLRRLfglpvspPRHYVPSSEGF 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 495778556  232 RQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSEVDII-MAWRRDS 279
Cdd:TIGR03298 226 VDAARAGLGWGMVPELQAEPHLAAGRLVELAPGRALDVPLYwHHWRLES 274
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 22-261 1.76e-07

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 51.46  E-value: 1.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEALARGWETHLTL 101
Cdd:NF040786  16 KSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 102 VTEAlVPTEALFP-LVDRLAAK-ANTQLSIITEVLAGAWERLETGRADIVIAPDMhfRSSSEINSRKLYSvMNVYVAAPN 179
Cdd:NF040786  96 GAST-IPGQYLLPeLLKKFKEKyPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK--LEKKRLVYTPFYK-DRLVLITPN 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 180 H----PIHQEPEPLSEVTRVKYrgvavadTARERPVLTVQLLDKQPR------------LTVTSLEDKRQALLAGLGVAT 243
Cdd:NF040786 172 GtekyRMLKEEISISELQKEPF-------IMREEGSGTRKEAEKALKslgisledlnvvASLGSTEAIKQSVEAGLGISV 244

                        250
                 ....*....|....*...
gi 495778556 244 MPYPFVEKDIAEGRLRVV 261
Cdd:NF040786 245 ISELAAEKEVERGRVLIF 262
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-84 1.54e-05

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 45.50  E-value: 1.54e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495778556  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKL 84
Cdd:NF041036  16 GSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSL 78
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 99-291 5.47e-55

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 176.69  E-value: 5.47e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  99 LTLVTEALVPTEALFPLVDRLAAKAN-TQLSIITEVLAGAWERLETGRADIVIAPDmHFRSSSEINSRKLYSVMNVYVAA 177
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKaTRIRLSEEVLGGTWDALASGRADLVIGAT-GELPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 178 PNHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGR 257
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495778556 258 LrvVSPEY---TSEVDIIMAWRRDSMGEAKSWCLREI 291
Cdd:cd08431  161 L--VEKALedpRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-288 1.11e-46

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 158.95  E-value: 1.11e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEA 90
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  91 LARGWETHLTLVTEALVPTEALFPLV-DRLAAKANTQLSIITEVLAGAWERLETGRADIVI-----AP---DMHFRSSSE 161
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIvDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatraIPvggRFAFRDMGM 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 162 INSRklysvmnvYVAAPNHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGV 241
Cdd:PRK11074 166 LSWA--------CVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCV 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 495778556 242 ATMPYPFVEKDIAEGRL---RVVSPEYTSEVdiIMAWRRDSMGEAKSWCL 288
Cdd:PRK11074 238 GMVPTHFAKPLINSGKLvelTLENPFPDSPC--CLTWQQNDMSPALAWLL 285
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-278 2.98e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.77  E-value: 2.98e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTT 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  87 DAEALARGWETHLTLVTEALVPTEALFPLVDRLAAKA-NTQLSIITEVLAGAWERLETGRADIVIAPDMHfrSSSEINSR 165
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRLVDALLEGELDLAIRLGPP--PDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 166 KLYSVMNVYVAAPNHPIhqepeplsevtrvkyrgvavadtARERPVltvqlldkqprltVTSLEDKRQALLAGLGVATMP 245
Cdd:COG0583  159 PLGEERLVLVASPDHPL-----------------------ARRAPL-------------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270
                 ....*....|....*....|....*....|....
gi 495778556 246 YPFVEKDIAEGRLRVVS-PEYTSEVDIIMAWRRD 278
Cdd:COG0583  203 RFLAADELAAGRLVALPlPDPPPPRPLYLVWRRR 236
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-297 5.16e-31

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 117.99  E-value: 5.16e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  10 EALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAE 89
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  90 ALARGWETHLTLVTEALV-PTEALFPLVDRLAAK-ANTQLSIITEVLAGAWERLETGRADIVIAPDMHFRSSSEINSRKL 167
Cdd:PRK10094  85 QVNDGVERQVNIVINNLLyNPQAVAQLLAWLNERyPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 168 YSVMNVYVAAPNHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATMPYP 247
Cdd:PRK10094 165 GSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKS 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495778556 248 FVEKDIAEGRL---RVVSPEYTSEVDIimAWRRDSMGEAKSwclrEIPKLFAH 297
Cdd:PRK10094 245 LCQSMIDNQQLvsrVIPTMRPPSPLSL--AWRKFGSGKAVE----DIVTLFTQ 291
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 2.75e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.95  E-value: 2.75e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556    9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 98-279 6.39e-13

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: 66.16  E-value: 6.39e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   98 HLTLVTEALVPTEALFPLVDRLAAKA-NTQLSIITEVLAGAWERLETGRADIVIApdMHFRSSSEINSRKLYSVMNVYVA 176
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYpDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  177 APNHPIHQ-EPEPLSEVTRVKY--RGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDI 253
Cdd:pfam03466  81 PPDHPLARgEPVSLEDLADEPLilLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180
                  ....*....|....*....|....*..
gi 495778556  254 AEGRLRVVS-PEYTSEVDIIMAWRRDS 279
Cdd:pfam03466 161 ADGRLVALPlPEPPLPRELYLVWRKGR 187
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-94 3.36e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 59.65  E-value: 3.36e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   8 TLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERG-RV--LLEAADKL 84
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnRIlaLCEETCRA 85

                         90
                 ....*....|
gi 495778556  85 TTDAEALARG 94
Cdd:CHL00180  86 LEDLKNLQRG 95
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-250 7.13e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 58.88  E-value: 7.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEaadKLTT 86
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  87 DAEALARGWETHLTLVTEALVPTEALFPLVDRLAAK-ANTQLSIITEVLAGAWERLETGRADIVIAPDMHFRSSSEinsr 165
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNwPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH---- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 166 klYSVMNVY----VAAPNHPIHQE----PEPLSEVTRVKYrgvavadtARERPVLTVQLLDKQPRLTVTSLEDKRQALL- 236
Cdd:PRK15421 155 --YSPMFDYevrlVLAPDHPLAAKtritPEDLASETLLIY--------PVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLl 224

                        250
                 ....*....|....*....
gi 495778556 237 -----AGLGVATMPYPFVE 250
Cdd:PRK15421 225 iqmvaARMGIAALPHWVVE 243
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 164-268 1.00e-09

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: 57.07  E-value: 1.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 164 SRKLYSVMNVYVAAP----NHPIHQEPEPLSEVTRVKYRGVAVADT---ARERPVLTVQLldkQPRLTVTSLEDKRQALL 236
Cdd:cd08422   64 ARRLGPVRRVLVASPaylaRHGTPQTPEDLARHRCLGYRLPGRPLRwrfRRGGGEVEVRV---RGRLVVNDGEALRAAAL 140

                         90       100       110
                 ....*....|....*....|....*....|..
gi 495778556 237 AGLGVATMPYPFVEKDIAEGRLRVVSPEYTSE 268
Cdd:cd08422  141 AGLGIALLPDFLVAEDLASGRLVRVLPDWRPP 172
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-258 1.03e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 58.32  E-value: 1.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGR----VLLEAADKL 84
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIReifdQLAEATRKL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  85 ttdaeaLARGWETHLTLvteALVPTEALFPLVDRLA--AKANTQLsiitEVLAGAWERLE-TGRADIVIAPDMHFRSSSE 161
Cdd:PRK11139  88 ------RARSAKGALTV---SLLPSFAIQWLVPRLSsfNEAHPDI----DVRLKAVDRLEdFLRDDVDVAIRYGRGNWPG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 162 INSRKLYSVMNVYVAAP-----NHPIHQePEPLSEVT------RVKYRgvAVADTARERPvLTVQlldKQPRLTVTSLed 230
Cdd:PRK11139 155 LRVEKLLDEYLLPVCSPallngGKPLKT-PEDLARHTllhddsREDWR--AWFRAAGLDD-LNVQ---QGPIFSHSSM-- 225

                        250       260
                 ....*....|....*....|....*...
gi 495778556 231 KRQALLAGLGVATMPYPFVEKDIAEGRL 258
Cdd:PRK11139 226 ALQAAIHGQGVALGNRVLAQPEIEAGRL 253
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 9-190 5.16e-09

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 56.12  E-value: 5.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGR-VL--LEAADKLT 85
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARrALqdLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  86 TDAEALARGwetHLTLvteALVPTEALF---PLVDRL-AAKANTQLSiITEVlagAWERLETG----RADIVIA-PDMHf 156
Cdd:PRK11242  83 HDVADLSRG---SLRL---AMTPTFTAYligPLIDAFhARYPGITLT-IREM---SQERIEALladdELDVGIAfAPVH- 151

                        170       180       190
                 ....*....|....*....|....*....|....
gi 495778556 157 rsSSEINSRKLYSVMNVYVAAPNHPIHQEPEPLS 190
Cdd:PRK11242 152 --SPEIEAQPLFTETLALVVGRHHPLAARRKALT 183
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 9-188 2.18e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 54.28  E-value: 2.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   9 LEALRVMDAIDRRG-SFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRtkFTNvgrmLLERGRVLLEAADKLTTD 87
Cdd:PRK12683   3 FQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKR--LTG----LTEPGKELLQIVERMLLD 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  88 AEALARGWET-------HLTLVTE------ALVPT----EALFPLVdRLAAKANTQLSIItevlagawERLETGRADIVI 150
Cdd:PRK12683  77 AENLRRLAEQfadrdsgHLTVATThtqaryALPKVvrqfKEVFPKV-HLALRQGSPQEIA--------EMLLNGEADIGI 147

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 495778556 151 APDMhFRSSSEINSRKLYSVMNVYVAAPNHPIHQEPEP 188
Cdd:PRK12683 148 ATEA-LDREPDLVSFPYYSWHHVVVVPKGHPLTGRENL 184
PRK12680 PRK12680
LysR family transcriptional regulator;
7-253 2.63e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 54.24  E-value: 2.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   7 LTLEALRVMDAI-DRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTK-FTNVGRMLLERGRVLLEAADKL 84
Cdd:PRK12680   1 MTLTQLRYLVAIaDAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  85 TTDAEALARGWETHLTLVTealVPTEALFPLVDRLAA--KANTQLSIITEVLA--GAWERLETGRADIVIAPDMHFRSSS 160
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTT---THTQARFVLPPAVAQikQAYPQVSVHLQQAAesAALDLLGQGDADIAIVSTAGGEPSA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 161 EInSRKLYSVMNVYVAAPNHPIHQ-----EPEPLSEVTRVKYRGVAVADTARERPVLTVQLldkQPRLTVTSLEDK--RQ 233
Cdd:PRK12680 158 GI-AVPLYRWRRLVVVPRGHALDTprrapDMAALAEHPLISYESSTRPGSSLQRAFAQLGL---EPSIALTALDADliKT 233

                        250       260
                 ....*....|....*....|...
gi 495778556 234 ALLAGLGV---ATMPYPFVEKDI 253
Cdd:PRK12680 234 YVRAGLGVgllAEMAVNANDEDL 256
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-60 5.98e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 53.08  E-value: 5.98e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495778556   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSgHR 60
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRS-HR 66
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 158-274 1.23e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 51.02  E-value: 1.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 158 SSSEINSRKLYSVMNVYVAAPN----HPIHQEPEPLSEvtrvkYRGVAVADTAR------ERPVLTVQLLDKQPRLTVTS 227
Cdd:cd08473   62 EDSSLVMRVLGQSRQRLVASPAllarLGRPRSPEDLAG-----LPTLSLGDVDGrhswrlEGPDGESITVRHRPRLVTDD 136

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 495778556 228 LEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSEVDIIMA 274
Cdd:cd08473  137 LLTLRQAALAGVGIALLPDHLCREALRAGRLVRVLPDWTPPRGIVHA 183
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-279 1.31e-07

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 51.84  E-value: 1.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRsGHRTKFTNVGRMLLERGR--VLLEAadKLTTDA 88
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARqvRLLEA--ELLAEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   89 EALARGWETHLTLVTEALVPTEALFPLVDRLAAKANTQLSIITEVLAGAWERLETGRAdiVIAPDMHFRSSSEINSRKLY 168
Cdd:TIGR03298  82 PGLAPGAPTRLTIAVNADSLATWFLPALAPVLAREGVLLDLVVEDQDHTAELLRSGEV--LGAVTTEAKPVPGCRVVPLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  169 SVMNVYVAAPnhPIHQepeplsevtrvKY--RGVaVADTARERPVLT--------VQLLDKQ-------PRLTVTSLEDK 231
Cdd:TIGR03298 160 AMRYLAVASP--AFAA-----------RYfpDGV-TAAALARAPVIVfnrkddlqDRFLRRLfglpvspPRHYVPSSEGF 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 495778556  232 RQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSEVDII-MAWRRDS 279
Cdd:TIGR03298 226 VDAARAGLGWGMVPELQAEPHLAAGRLVELAPGRALDVPLYwHHWRLES 274
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 9-283 1.72e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 51.69  E-value: 1.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKlttdA 88
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEK----A 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  89 EALARGWETHLTLVTEALVPTEA--LFPLV--DRLAAKANTQLSIITEVLAGAWERLETGRADI-VIAPDMHfrsSSEIN 163
Cdd:PRK09906  79 KLRARKIVQEDRQLTIGFVPSAEvnLLPKVlpMFRLRHPDTLIELVSLITTQQEEKLRRGELDVgFMRHPVY---SDEID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 164 SRKLYSVMNVYVAAPNHPIHQEPE-PLSEVTRVKYrgvaVADTARERPVLTVQLLD------KQPRL--TVTSLEDKRQA 234
Cdd:PRK09906 156 YLELLDEPLVVVLPVDHPLAHEKEiTAAQLDGVNF----ISTDPAYSGSLAPIIKAwfaqhnSQPNIvqVATNILVTMNL 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495778556 235 LLAGLGVATMPY---PFVEKDIAEGRLRVVSPeytsEVDIIMAWRRDSMGEA 283
Cdd:PRK09906 232 VGMGLGCTIIPGymnNFNTGQVVFRPLAGNVP----SIALLMAWKKGEMKPA 279
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 22-261 1.76e-07

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 51.46  E-value: 1.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEALARGWETHLTL 101
Cdd:NF040786  16 KSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 102 VTEAlVPTEALFP-LVDRLAAK-ANTQLSIITEVLAGAWERLETGRADIVIAPDMhfRSSSEINSRKLYSvMNVYVAAPN 179
Cdd:NF040786  96 GAST-IPGQYLLPeLLKKFKEKyPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK--LEKKRLVYTPFYK-DRLVLITPN 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 180 H----PIHQEPEPLSEVTRVKYrgvavadTARERPVLTVQLLDKQPR------------LTVTSLEDKRQALLAGLGVAT 243
Cdd:NF040786 172 GtekyRMLKEEISISELQKEPF-------IMREEGSGTRKEAEKALKslgisledlnvvASLGSTEAIKQSVEAGLGISV 244

                        250
                 ....*....|....*...
gi 495778556 244 MPYPFVEKDIAEGRLRVV 261
Cdd:NF040786 245 ISELAAEKEVERGRVLIF 262
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 124-278 2.75e-07

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: 49.91  E-value: 2.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 124 NTQLSIITEVLAGAWERLETGRADIVIApdMHFRSSSEINSRKLYSVMNVYVAAPNHPIHQEPE-PLSEVTRVKYrgVAV 202
Cdd:cd05466   28 GVELSLVEGGSSELLEALLEGELDLAIV--ALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSvTLADLADEPL--ILF 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 203 ADTARERPVLTVQLLDK----QPRLTVTSLEDKRQALLAGLGVATMPYPFVEkDIAEGRLRVVSPEYTS-EVDIIMAWRR 277
Cdd:cd05466  104 ERGSGLRRLLDRAFAEAgftpNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPLEDPPlSRTIGLVWRK 182


                 .
gi 495778556 278 D 278
Cdd:cd05466  183 G 183
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-94 2.78e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 50.84  E-value: 2.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAAdkltT 86
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQA----V 78


                 ....*...
gi 495778556  87 DAEALARG 94
Cdd:PRK10837  79 EIEQLFRE 86
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 109-277 1.15e-06

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: 48.36  E-value: 1.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 109 TEALF--PLVDRLAAKA-NTQLSIITEVLAGAWERLETGRADIVIapDMHFRSSSEINSRKLYSVMNVYVAAPNHPIHQE 185
Cdd:cd08417   10 LEALLlpPLLARLRQEApGVRLRFVPLDRDDLEEALESGEIDLAI--GVFPELPPGLRSQPLFEDRFVCVARKDHPLAGG 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 186 PEPLSEVTRvkYRGVAVADTARERPV----LTVQLLDKQPRLTVTSLedkrQALLAGLG----VATMPYPFVEKDIAEGR 257
Cdd:cd08417   88 PLTLEDYLA--APHVLVSPRGRGHGLvddaLAELGLSRRVALTVPHF----LAAPALVAgtdlIATVPRRLAEALAERLG 161

                        170       180
                 ....*....|....*....|.
gi 495778556 258 LRVVSPEY-TSEVDIIMAWRR 277
Cdd:cd08417  162 LRVLPLPFeLPPFTVSLYWHP 182
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 220-267 3.14e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 47.07  E-value: 3.14e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 495778556 220 QPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTS 267
Cdd:cd08474  129 EGPLILNDSDLMLDAALDGLGIAYLFEDLVAEHLASGRLVRVLEDWSP 176
PRK09801 PRK09801
LysR family transcriptional regulator;
12-276 1.01e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 46.18  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  12 LRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAeal 91
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV--- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  92 argweTHLTLVTEALVPTEALFPLVDRLAAKANTQLSIITEVLAGAWERLETgRADIVIAP-DMHFRSSSEINSRKLYSV 170
Cdd:PRK09801  88 -----TQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDR-QIDLVQDNiDLDIRINDEIPDYYIAHL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 171 MN----VYVAAPNH-PIHQEPEPLSEVTR-----VKYR----GVAVADTARERPVLTVqlldkQPRLTVTSLEDKRQALL 236
Cdd:PRK09801 162 LTknkrILCAAPEYlQKYPQPQSLQELSRhdclvTKERdmthGIWELGNGQEKKSVKV-----SGHLSSNSGEIVLQWAL 236

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 495778556 237 AGLGVATMPYPFVEKDIAEGRLRVVSPEYTSEVDIIMAWR 276
Cdd:PRK09801 237 EGKGIMLRSEWDVLPFLESGKLVQVLPEYAQSANIWAVYR 276
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-84 1.54e-05

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 45.50  E-value: 1.54e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495778556  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKL 84
Cdd:NF041036  16 GSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSL 78
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 165-265 2.17e-05

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


Pssm-ID: 176160  Cd Length: 201  Bit Score: 44.44  E-value: 2.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 165 RKLYSVMNVYVAAP----NHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVTSLEDKRQALLAGLG 240
Cdd:cd08471   65 TRVGSVRRVVCASPaylaRHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLG 144

                         90       100
                 ....*....|....*....|....*
gi 495778556 241 VATMPYPFVEKDIAEGRLRVVSPEY 265
Cdd:cd08471  145 LTRVLSYQVAEELAAGRLQRVLEDF 169
PRK09986 PRK09986
LysR family transcriptional regulator;
1-101 3.15e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 44.71  E-value: 3.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   1 MAKERALTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEA 80
Cdd:PRK09986   1 MERLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN 80

                         90       100
                 ....*....|....*....|.
gi 495778556  81 ADKLTTDAEALARGWETHLTL 101
Cdd:PRK09986  81 AEQSLARVEQIGRGEAGRIEI 101
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 22-274 3.23e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.60  E-value: 3.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLL---EAADKLTTDAEALARGweth 98
Cdd:PRK14997  17 GGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQDAIAALQVEPRG---- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  99 ltlVTEALVPTEALFPLVDRLAAKANTQLSIITEVLAGAWERLETGRADIVIAPDMHFR--SSSEINSRKLYSVMNVYVA 176
Cdd:PRK14997  93 ---IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRpfEDSDLVMRVLADRGHRLFA 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 177 APNHpIHQEPEPLSEVTRVKYRGVAVADTareRPVLTVQLLDKQ---------PRLTVTSLEDKRQALLAGLGVATMPYP 247
Cdd:PRK14997 170 SPDL-IARMGIPSAPAELSHWPGLSLASG---KHIHRWELYGPQgaraevhftPRMITTDMLALREAAMAGVGLVQLPVL 245

                        250       260
                 ....*....|....*....|....*..
gi 495778556 248 FVEKDIAEGRLRVVSPEYTSEVDIIMA 274
Cdd:PRK14997 246 MVKEQLAAGELVAVLEEWEPRREVIHA 272
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 221-266 3.34e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 43.76  E-value: 3.34e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495778556 221 PRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYT 266
Cdd:cd08477  125 GRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLVELLPDYL 170
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-81 3.61e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 44.75  E-value: 3.61e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAA 81
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEV 76
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-86 1.30e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTT 86
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 157-268 1.75e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 41.73  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 157 RSSSEInSRKLYSVMNVYVAAPN----HPIHQEPEPLSEVTRVKY-----RGVAVADTARERPVLTVQLldkQPRLTVTS 227
Cdd:cd08472   58 ADSSLV-ARRLGELRMVTCASPAylarHGTPRHPEDLERHRAVGYfsartGRVLPWEFQRDGEEREVKL---PSRVSVND 133

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 495778556 228 LEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSE 268
Cdd:cd08472  134 SEAYLAAALAGLGIIQVPRFMVRPHLASGRLVEVLPDWRPP 174
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 220-275 4.04e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 40.62  E-value: 4.04e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495778556 220 QPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSE-VDIIMAW 275
Cdd:cd08475  126 APRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPEgLPIHAVW 182
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-72 6.28e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.57  E-value: 6.28e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 495778556  35 PSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLE 72
Cdd:PRK11716   5 PSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRP 42
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 233-258 1.04e-03

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: 39.49  E-value: 1.04e-03
                         10        20
                 ....*....|....*....|....*.
gi 495778556 233 QALLAGLGVATMPYPFVEKDIAEGRL 258
Cdd:cd08432  134 QAAVAGLGVALAPRALVADDLAAGRL 159
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 173-260 1.75e-03

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: 38.64  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 173 VYVAAPNHPIHQEpeplsevtrvkyRGVAVADTARERPVL------TVQLLDK---------QPRLTVTSLEDKRQALLA 237
Cdd:cd08419   74 VVIAPPDHPLAGQ------------KRIPLERLAREPFLLrepgsgTRLAMERffaehgvtlRVRMELGSNEAIKQAVMA 141

                         90       100
                 ....*....|....*....|...
gi 495778556 238 GLGVATMPYPFVEKDIAEGRLRV 260
Cdd:cd08419  142 GLGLSVLSLHTLALELATGRLAV 164
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 223-268 2.91e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 37.99  E-value: 2.91e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495778556 223 LTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSE 268
Cdd:cd08476  127 LVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEE 172
PRK09791 PRK09791
LysR family transcriptional regulator;
9-79 2.94e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 38.59  E-value: 2.94e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495778556   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLE 79
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILE 77
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
9-190 3.49e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 38.42  E-value: 3.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556   9 LEALRVMDAIDRRG-SFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTkftnvgRMLLERGRVLLEAADKLTTD 87
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRL------RGLTEPGRIILASVERILQE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556  88 AEALAR-GWE------THLTLVTEALVPTEALFPLVDRLAAK-ANTQLSIITEVLAGAWERLETGRADIVIAPDmHFRSS 159
Cdd:PRK12684  77 VENLKRvGKEfaaqdqGNLTIATTHTQARYALPAAIKEFKKRyPKVRLSILQGSPTQIAEMVLHGQADLAIATE-AIADY 155

                        170       180       190
                 ....*....|....*....|....*....|.
gi 495778556 160 SEINSRKLYSVMNVYVAAPNHPIHQEpEPLS 190
Cdd:PRK12684 156 KELVSLPCYQWNHCVVVPPDHPLLER-KPLT 185
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 233-258 4.65e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 37.38  E-value: 4.65e-03
                         10        20
                 ....*....|....*....|....*.
gi 495778556 233 QALLAGLGVATMPYPFVEKDIAEGRL 258
Cdd:cd08482  137 EAAVAGLGVAIAPWPLVRDDLASGRL 162
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 215-269 6.29e-03

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 36.93  E-value: 6.29e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495778556 215 QLLDKQPRLTVTSLEDKRQALLAGLGVATMPYPFVEKDIAEGRLRVVSPEYTSEV 269
Cdd:cd08478  120 NLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFAEQTSDV 174
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 24-79 8.39e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 37.32  E-value: 8.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495778556  24 FAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGR-VLLE 79
Cdd:PRK11151  18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARtVLRE 74
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 173-261 9.35e-03

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: 36.70  E-value: 9.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778556 173 VYVAAPNHPIHQEPEPLSE-------VTRVKYRGV-AVADTARERpvLTVQLLDKQPRLTVTSLEDKRQALLAGLGVATM 244
Cdd:cd08420   75 VLVVPPDHPLAGRKEVTAEelaaepwILREPGSGTrEVFERALAE--AGLDGLDLNIVMELGSTEAIKEAVEAGLGISIL 152

                         90
                 ....*....|....*..
gi 495778556 245 PYPFVEKDIAEGRLRVV 261
Cdd:cd08420  153 SRLAVRKELELGRLVAL 169
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH