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Conserved domains on  [gi|1596946267|gb|TDW02150|]
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LysR family transcriptional regulator [Vibrio crassostreae]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 20370986)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 95-291 4.25e-70

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: 215.38  E-value: 4.25e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGyLGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08422     1 GRLRISAPVS-FGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCLT----GSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGyrlpGRPLRWRFRRGG---GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946267 251 LNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR_Sec_metab super family cl49002
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-163 6.48e-25

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.


The actual alignment was detected with superfamily member NF040786:

Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 101.15  E-value: 6.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALI 84
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 AAVDDVEEVRGDIKVNcVGGYLGEVIIADLVNEFMQLYPDISISLDFS-SNRV--DLIEDAFDIAFRMGSLEDAGFIARK 161
Cdd:NF040786   81 EFDRYGKESKGVLRIG-ASTIPGQYLLPELLKKFKEKYPNVRFKLMISdSIKVieLLLEGEVDIGFTGTKLEKKRLVYTP 159


                  ..
gi 1596946267 162 LL 163
Cdd:NF040786  160 FY 161
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 95-291 4.25e-70

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: 215.38  E-value: 4.25e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGyLGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08422     1 GRLRISAPVS-FGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCLT----GSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGyrlpGRPLRWRFRRGG---GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946267 251 LNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-297 7.50e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 198.94  E-value: 7.50e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALI 84
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 AAVDDVEEVRGDIKVNCVGGyLGEVIIADLVNEFMQLYPDISISLDF-SSNRV--DLIEDAFDIAFRMGSLEDAGFIARK 161
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPS-LARYLLPPLLARFRARHPGVRLELREgNSDRLvdALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 162 LLDIEMGTLASPEYfarkgkpnhpkDLIHHDCLTGSVrkwsfqapddtkktvdvhvtgrlqckngRVLVQGAKSGNGIIR 241
Cdd:COG0583   160 LGEERLVLVASPDH-----------PLARRAPLVNSL----------------------------EALLAAVAAGLGIAL 200

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1596946267 242 VPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRFER 297
Cdd:COG0583   201 LPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 6-298 1.62e-44

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 153.22  E-value: 1.62e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   6 NLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALIA 85
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  86 AVDDVEEVRGDIKVNCVGGYLgEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRM--GSLEDAGFIARKLL 163
Cdd:PRK14997   83 IAALQVEPRGIVKLTCPVTLL-HVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLVMRVLA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 164 DIEMGTLASPEYFARKGKPNHPKDLIHHDCLT-GS---VRKWSFQAPDDTKktVDVHVTGRLQCKNGRVLVQGAKSGNGI 239
Cdd:PRK14997  162 DRGHRLFASPDLIARMGIPSAPAELSHWPGLSlASgkhIHRWELYGPQGAR--AEVHFTPRMITTDMLALREAAMAGVGL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1596946267 240 IRVPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRFERM 298
Cdd:PRK14997  240 VQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYARM 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-295 2.41e-32

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: 118.55  E-value: 2.41e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  94 RGDIKVNCVGgYLGEVIIADLVNEFMQLYPDISISL--DFSSNRVDLIED-AFDIAFRMGSLEDAGFIARKLLDIEMGTL 170
Cdd:pfam03466   1 SGRLRIGAPP-TLASYLLPPLLARFRERYPDVELELteGNSEELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 171 ASPEYFARKGKPNHPKDLIHHDCLTGSVRKWSFQAPDDTKKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1596946267 251 LNDGQL-EQVFDEWVVPkVDFSAIYHRDRYQPSRIRTFIDFVKDRF 295
Cdd:pfam03466 160 LADGRLvALPLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREAL 204
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-163 6.48e-25

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: 101.15  E-value: 6.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALI 84
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 AAVDDVEEVRGDIKVNcVGGYLGEVIIADLVNEFMQLYPDISISLDFS-SNRV--DLIEDAFDIAFRMGSLEDAGFIARK 161
Cdd:NF040786   81 EFDRYGKESKGVLRIG-ASTIPGQYLLPELLKKFKEKYPNVRFKLMISdSIKVieLLLEGEVDIGFTGTKLEKKRLVYTP 159


                  ..
gi 1596946267 162 LL 163
Cdd:NF040786  160 FY 161
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 1.14e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 91.29  E-value: 1.14e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-166 1.19e-21

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 92.33  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGqDLYARC-EQALDNIDQAlIA 85
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAG-EVYLRYaRRALQDLEAG-RR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  86 AVDDVEEV-RGDIKVnCVGGYLGEVIIADLVNEFMQLYPDISISLD-FSSNRVD--LIEDAFDIAFrmgsledaGFIARK 161
Cdd:PRK11242   81 AIHDVADLsRGSLRL-AMTPTFTAYLIGPLIDAFHARYPGITLTIReMSQERIEalLADDELDVGI--------AFAPVH 151


                  ....*
gi 1596946267 162 LLDIE 166
Cdd:PRK11242  152 SPEIE 156
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
1-91 1.69e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 41.11  E-value: 1.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   1 MLNQINLSDIRSFVL--IARLG--NFTKAAEELDVSRSHVSRQVSSLEKQmGvtlFIRTTR--------TLRLTHAGQDL 68
Cdd:COG1846    30 ALAELGLTPAQFRVLaaLAEAGglTQSELAERLGLTKSTVSRLLDRLEEK-G---LVEREPdpedrravLVRLTEKGRAL 105

                          90       100
                  ....*....|....*....|...
gi 1596946267  69 YARCEQALDNIDQALIAAVDDVE 91
Cdd:COG1846   106 LEEARPALEALLAELLAGLSEEE 128
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
5-91 1.11e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.57  E-value: 1.11e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267    5 INLSDIRSFVLIARLG--NFTKAAEELDVSRSHVSRQVSSLEKqMGvtlFIRTTR--------TLRLTHAGQDLYARCEQ 74
Cdd:smart00347   8 LTPTQFLVLRILYEEGplSVSELAKRLGVSPSTVTRVLDRLEK-KG---LVRREPspedrrsvLVSLTEEGRELIEQLLE 83

                           90
                   ....*....|....*..
gi 1596946267   75 ALDNIDQALIAAVDDVE 91
Cdd:smart00347  84 ARSETLAELLAGLTAEE 100
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 95-291 4.25e-70

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: 215.38  E-value: 4.25e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGyLGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08422     1 GRLRISAPVS-FGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCLT----GSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:cd08422    80 YLARHGTPQTPEDLARHRCLGyrlpGRPLRWRFRRGG---GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946267 251 LNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-297 7.50e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 198.94  E-value: 7.50e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALI 84
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 AAVDDVEEVRGDIKVNCVGGyLGEVIIADLVNEFMQLYPDISISLDF-SSNRV--DLIEDAFDIAFRMGSLEDAGFIARK 161
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPS-LARYLLPPLLARFRARHPGVRLELREgNSDRLvdALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 162 LLDIEMGTLASPEYfarkgkpnhpkDLIHHDCLTGSVrkwsfqapddtkktvdvhvtgrlqckngRVLVQGAKSGNGIIR 241
Cdd:COG0583   160 LGEERLVLVASPDH-----------PLARRAPLVNSL----------------------------EALLAAVAAGLGIAL 200

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1596946267 242 VPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRFER 297
Cdd:COG0583   201 LPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-291 1.82e-55

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: 178.19  E-value: 1.82e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGYlGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08477     1 GKLRISAPVTF-GSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCL----TGSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:cd08477    80 YLARHGTPTTPEDLARHECLgfsyWRARNRWRLEGPG---GEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946267 251 LNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08477   157 LASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-293 1.76e-50

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 165.56  E-value: 1.76e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGYlGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08470     1 GLLRITCPVAY-GERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCLTGSVRKWSFQapdDTKKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDG 254
Cdd:cd08470    80 YLERHGTPHSLADLDRHNCLLGTSDHWRFQ---ENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAG 156

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1596946267 255 QLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKD 293
Cdd:cd08470   157 RLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 6-298 1.62e-44

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 153.22  E-value: 1.62e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   6 NLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALIA 85
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  86 AVDDVEEVRGDIKVNCVGGYLgEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRM--GSLEDAGFIARKLL 163
Cdd:PRK14997   83 IAALQVEPRGIVKLTCPVTLL-HVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLVMRVLA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 164 DIEMGTLASPEYFARKGKPNHPKDLIHHDCLT-GS---VRKWSFQAPDDTKktVDVHVTGRLQCKNGRVLVQGAKSGNGI 239
Cdd:PRK14997  162 DRGHRLFASPDLIARMGIPSAPAELSHWPGLSlASgkhIHRWELYGPQGAR--AEVHFTPRMITTDMLALREAAMAGVGL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1596946267 240 IRVPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRFERM 298
Cdd:PRK14997  240 VQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYARM 298
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 7.53e-41

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 140.42  E-value: 7.53e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGYlGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08479     1 GLLRVNASFGF-GRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCLT-----GSVRKWSFqapDDTKKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQ 249
Cdd:cd08479    80 YLERHGAPASPEDLARHDCLVirendEDFGLWRL---RNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAP 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946267 250 ELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDF 290
Cdd:cd08479   157 YLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDF 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-295 5.09e-40

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: 138.43  E-value: 5.09e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 107 GEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGKPNHPK 186
Cdd:cd08471    12 GRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAYLARHGTPKHPD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 187 DLIHHDCLTGSV----RKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDE 262
Cdd:cd08471    92 DLADHDCIAFTGlspaPEWRFREGG---KERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAAGRLQRVLED 168

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1596946267 263 WVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRF 295
Cdd:cd08471   169 FEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 110-291 1.96e-39

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: 137.08  E-value: 1.96e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 110 IIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGKPNHPKDLI 189
Cdd:cd08478    17 LLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHGTPQSIEDLA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 190 HHDCL----TGSVRKWSFQAPDDTKktvdVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEWVV 265
Cdd:cd08478    97 QHQLLgftePASLNTWPIKDADGNL----LKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFAEQTS 172

                         170       180
                  ....*....|....*....|....*..
gi 1596946267 266 P-KVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08478   173 DvRQPINAVYYRNTALSLRIRCFIDFL 199
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-291 4.49e-39

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: 135.84  E-value: 4.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 115 VNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGKPNHPKDLIHHDCL 194
Cdd:cd08476    18 LAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHGTPETPADLAEHACL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 195 ------TGSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEWVVPKV 268
Cdd:cd08476    98 ryrfptTGKLEPWPLRGDG---GDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEERG 174

                         170       180
                  ....*....|....*....|...
gi 1596946267 269 DFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08476   175 QFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-291 1.13e-38

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: 134.90  E-value: 1.13e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  94 RGDIKVNcVGGYLGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLL-DIEMGTLAS 172
Cdd:cd08474     2 AGTLRIN-APRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGpPLRMAVVAS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 173 PEYFARKGKPNHPKDLIHHDCL------TGSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIY 246
Cdd:cd08474    81 PAYLARHGTPEHPRDLLNHRCIryrfptSGALYRWEFERGG---RELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1596946267 247 CLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08474   158 VAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 117-294 1.62e-38

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: 134.56  E-value: 1.62e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 117 EFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGKPNHPKDLIHHDC--- 193
Cdd:cd08472    22 DFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAYLARHGTPRHPEDLERHRAvgy 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 194 ---LTGSVRKWSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEWVVPKVDF 270
Cdd:cd08472   102 fsaRTGRVLPWEFQRDG---EEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLASGRLVEVLPDWRPPPLPV 178

                         170       180
                  ....*....|....*....|....
gi 1596946267 271 SAIYHRDRYQPSRIRTFIDFVKDR 294
Cdd:cd08472   179 SLLYPHRRHLSPRVRVFVDWVAEL 202
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 2.56e-36

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176169  Cd Length: 198  Bit Score: 128.99  E-value: 2.56e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  95 GDIKVNCVGGYlGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPE 174
Cdd:cd08480     1 GRLRVNASVPF-GTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 175 YFARKGKPNHPKDLIHHDCLTGSVRK----WSFQAPDdtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:cd08480    80 YLARHGTPLTPQDLARHNCLGFNFRRalpdWPFRDGG---RIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADD 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946267 251 LNDGQLEQVFDEWVVPKV-DFSAIYHRDRYQPSRIRTFIDF 290
Cdd:cd08480   157 IAAGRLVPVLEEYNPGDRePIHAVYVGGGRLPARVRAFLDF 197
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-289 1.30e-35

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: 126.90  E-value: 1.30e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 111 IADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLED-AGFIARKLLDIEMGTLASPEYFARKGKPNHPKDLI 189
Cdd:cd08475    16 VAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADsTGLVARRLGTQRMVLCASPAYLARHGTPRTLEDLA 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 190 HHDCLT----GSVRKWSFQAPDDtkKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEWVV 265
Cdd:cd08475    96 EHQCIAygrgGQPLPWRLADEQG--RLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAP 173

                         170       180
                  ....*....|....*....|....
gi 1596946267 266 PKVDFSAIYHRDRYQPSRIRTFID 289
Cdd:cd08475   174 EGLPIHAVWPRTRHLPPKVRAAVD 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 7-297 7.31e-34

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 125.34  E-value: 7.31e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDnidqALIAA 86
Cdd:PRK11139    8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFD----QLAEA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  87 VDDVEEvRGDIKVncvggylgeVIIADL-----------VNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDA 155
Cdd:PRK11139   84 TRKLRA-RSAKGA---------LTVSLLpsfaiqwlvprLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWP 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 156 GFIARKLLDIEMGTLASPEYFARKGKPNHPKDLIHHDCL-TGSVRKWsfQAPDDTKKTVDVHVTGRLQCKNGRVLVQGAK 234
Cdd:PRK11139  154 GLRVEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLhDDSREDW--RAWFRAAGLDDLNVQQGPIFSHSSMALQAAI 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1596946267 235 SGNGIIRVPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRFER 297
Cdd:PRK11139  232 HGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
13-298 2.47e-33

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 124.10  E-value: 2.47e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  13 FVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALdnidqaliAAVDDVEE 92
Cdd:PRK10632   10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRML--------HEVQDVHE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  93 --------VRGDIKVNCvGGYLGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLD 164
Cdd:PRK10632   82 qlyafnntPIGTLRIGC-SSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 165 IEMGTLASPEYFARKGKPNHPKDLIHHDCLTGSVR---KWSFQAPDDTkkTVDVHVTGRLQCKNGRVLVQGAKSGNGIIR 241
Cdd:PRK10632  161 MPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRpdnEFELIAPEGI--STRLIPQGRFVTNDPQTLVRWLTAGAGIAY 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1596946267 242 VPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFVKDRFERM 298
Cdd:PRK10632  239 VPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFVEV 295
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-290 2.61e-33

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: 121.12  E-value: 2.61e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  94 RGDIKVNCVGGyLGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAF--RMGSLEDAGFIARKLLDIEMGTLA 171
Cdd:cd08473     2 RGTVRVSCPPA-LAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvRFPPLEDSSLVMRVLGQSRQRLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 172 SPEYFARKGKPNHPKDLIHHDCL-TGSVR---KWSFQAPDDTKKTvdVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYC 247
Cdd:cd08473    81 SPALLARLGRPRSPEDLAGLPTLsLGDVDgrhSWRLEGPDGESIT--VRHRPRLVTDDLLTLRQAALAGVGIALLPDHLC 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1596946267 248 LQELNDGQLEQVFDEWVVPKVDFSAIYhrdryqPSR------IRTFIDF 290
Cdd:cd08473   159 REALRAGRLVRVLPDWTPPRGIVHAVF------PSRrgllpaVRALIDF 201
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-295 2.41e-32

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: 118.55  E-value: 2.41e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  94 RGDIKVNCVGgYLGEVIIADLVNEFMQLYPDISISL--DFSSNRVDLIED-AFDIAFRMGSLEDAGFIARKLLDIEMGTL 170
Cdd:pfam03466   1 SGRLRIGAPP-TLASYLLPPLLARFRERYPDVELELteGNSEELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 171 ASPEYFARKGKPNHPKDLIHHDCLTGSVRKWSFQAPDDTKKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQE 250
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1596946267 251 LNDGQL-EQVFDEWVVPkVDFSAIYHRDRYQPSRIRTFIDFVKDRF 295
Cdd:pfam03466 160 LADGRLvALPLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREAL 204
PRK09801 PRK09801
LysR family transcriptional regulator;
1-292 3.97e-31

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 118.21  E-value: 3.97e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   1 MLNQINLS-DIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYarcEQALDNI 79
Cdd:PRK09801    1 MLNSWPLAkDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY---EHALEIL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  80 DQaLIAAVDDVEEVR----GDIKVNCVGGYlGEVIIADLVNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDA 155
Cdd:PRK09801   78 TQ-YQRLVDDVTQIKtrpeGMIRIGCSFGF-GRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPD 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 156 GFIARKLLDIEMGTLASPEYFARKGKPNHPKDLIHHDCLTGSVRK-----WSFQAPDDTKKtvdVHVTGRLQCKNGRVLV 230
Cdd:PRK09801  156 YYIAHLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDmthgiWELGNGQEKKS---VKVSGHLSSNSGEIVL 232

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1596946267 231 QGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEWvVPKVDFSAIYHRDRYQPSRIRTFIDFVK 292
Cdd:PRK09801  233 QWALEGKGIMLRSEWDVLPFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRVCVEFLA 293
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-163 6.48e-25

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: 101.15  E-value: 6.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALI 84
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 AAVDDVEEVRGDIKVNcVGGYLGEVIIADLVNEFMQLYPDISISLDFS-SNRV--DLIEDAFDIAFRMGSLEDAGFIARK 161
Cdd:NF040786   81 EFDRYGKESKGVLRIG-ASTIPGQYLLPELLKKFKEKYPNVRFKLMISdSIKVieLLLEGEVDIGFTGTKLEKKRLVYTP 159


                  ..
gi 1596946267 162 LL 163
Cdd:NF040786  160 FY 161
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 1.14e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 91.29  E-value: 1.14e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-166 1.19e-21

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 92.33  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGqDLYARC-EQALDNIDQAlIA 85
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAG-EVYLRYaRRALQDLEAG-RR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  86 AVDDVEEV-RGDIKVnCVGGYLGEVIIADLVNEFMQLYPDISISLD-FSSNRVD--LIEDAFDIAFrmgsledaGFIARK 161
Cdd:PRK11242   81 AIHDVADLsRGSLRL-AMTPTFTAYLIGPLIDAFHARYPGITLTIReMSQERIEalLADDELDVGI--------AFAPVH 151


                  ....*
gi 1596946267 162 LLDIE 166
Cdd:PRK11242  152 SPEIE 156
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-208 1.26e-21

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 92.37  E-value: 1.26e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   2 LNQINLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQ 81
Cdd:PRK10086   11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  82 ALIaavddveevrgDIKVNCVGGYL---GEVIIAD--LV---NEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLE 153
Cdd:PRK10086   91 EIL-----------DIKNQELSGTLtvySRPSIAQcwLVprlADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAP 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1596946267 154 DAGFIARKLLDIEMGTLASPEYFARKGKPNHPKDLIH----HDcltgsVRKWSFQAPDD 208
Cdd:PRK10086  160 SAQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHctllHD-----RQAWSNDSGTD 213
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 117-289 9.40e-20

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: 84.94  E-value: 9.40e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 117 EFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGkPNHPKDLIHHDCLTG 196
Cdd:cd08432    21 RFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLP-LLSPADLARHTLLHD 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 197 SVRKWSFQAPDDTKKTVDVHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEWVVPKVDFSAIYHR 276
Cdd:cd08432   100 ATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLVYPP 179

                         170
                  ....*....|...
gi 1596946267 277 DRYQPSRIRTFID 289
Cdd:cd08432   180 GRAESPAVAAFRD 192
PRK09986 PRK09986
LysR family transcriptional regulator;
2-162 2.44e-17

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 80.15  E-value: 2.44e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   2 LNQINLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQ 81
Cdd:PRK09986    4 LYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  82 ALiaavDDVEEV-RGD---IKVNCVGGYL-GEVIIAdlVNEFMQLYPDISISLD--FSSNRVDLIED-AFDIAF-RMGSL 152
Cdd:PRK09986   84 SL----ARVEQIgRGEagrIEIGIVGTALwGRLRPA--MRHFLKENPNVEWLLRelSPSMQMAALERrELDAGIwRMADL 157

                         170
                  ....*....|.
gi 1596946267 153 E-DAGFIARKL 162
Cdd:PRK09986  158 EpNPGFTSRRL 168
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-80 1.50e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 72.53  E-value: 1.50e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1596946267  10 IRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNID 80
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-135 2.49e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.97  E-value: 2.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDL--YARCEQAL-DNIDQAL 83
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLlrYGNRILALcEETCRAL 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1596946267  84 iaavDDVEEV-RGDIKVNC---VGGYLGEVIIAdlvnEFMQLYPDISISLDFSSNR 135
Cdd:CHL00180   87 ----EDLKNLqRGTLIIGAsqtTGTYLMPRLIG----LFRQRYPQINVQLQVHSTR 134
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 110-291 2.42e-13

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: 67.24  E-value: 2.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 110 IIADLVNEFMQLYPDISISLDFSSNRV---DLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGKPNHPK 186
Cdd:cd05466    14 LLPPLLAAFRQRYPGVELSLVEGGSSElleALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 187 DLIHHDCLTgsvrkwsFQAPDDTKKTVD-------VHVTGRLQCKNGRVLVQGAKSGNGIIRVPTIYClQELNDGQLEQV 259
Cdd:cd05466    94 DLADEPLIL-------FERGSGLRRLLDrafaeagFTPNIALEVDSLEAIKALVAAGLGIALLPESAV-EELADGGLVVL 165

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1596946267 260 FDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd05466   166 PLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09791 PRK09791
LysR family transcriptional regulator;
1-192 1.23e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.09  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   1 MLNQINLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNid 80
Cdd:PRK09791    1 MAFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEE-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  81 qaLIAAVDDVEEVRGDI--KVNC-VGGYLGEVIIADLVNEFMQLYPDISISLdFSSNRVDLI------EDAFDIAFRMGS 151
Cdd:PRK09791   79 --LRAAQEDIRQRQGQLagQINIgMGASIARSLMPAVISRFHQQHPQVKVRI-MEGQLVSMInelrqgELDFTINTYYQG 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1596946267 152 LEDAGFIARKLLDIEMGTlaspeyFARKGkpnHP-------KDLIHHD 192
Cdd:PRK09791  156 PYDHEFTFEKLLEKQFAV------FCRPG---HPaigarslKQLLDYS 194
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 117-261 1.79e-10

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 59.10  E-value: 1.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 117 EFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKgkpNHPKDLIhHDCLTG 196
Cdd:cd08487    21 EFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIAKRL---SHPADLI-NETLLR 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1596946267 197 SVR--KWS--FQAPDDTKKTvdvhVTGRLqCKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFD 261
Cdd:cd08487    97 SYRtdEWLqwFEAANMPPIK----IRGPV-FDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQPFK 160
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-87 1.89e-10

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 60.47  E-value: 1.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYA-------RCEQA-- 75
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTharailrQCEQAql 80

                          90
                  ....*....|...
gi 1596946267  76 -LDNIDQALIAAV 87
Cdd:PRK11233   81 aVHNVGQALSGQV 93
PRK10341 PRK10341
transcriptional regulator TdcA;
2-129 4.97e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 59.49  E-value: 4.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   2 LNQINLSDIRSFVL---IARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEqaldN 78
Cdd:PRK10341    1 MSTILLPKTQHLVVfqeVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSE----S 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1596946267  79 IDQALIAAVDDVEEVRGDIKVNCVGGY---LGEVIIADLVNEFMQLYPDISISL 129
Cdd:PRK10341   77 ITREMKNMVNEINGMSSEAVVDVSFGFpslIGFTFMSDMINKFKEVFPKAQVSM 130
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-174 1.34e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.78  E-value: 1.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARceqALDNIDQALi 84
Cdd:PRK10837    3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPR---ALALLEQAV- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 aavdDVEEV-RGD---IKV---NCVGGYLGEVIIAdlvnEFMQLYPDISISLDFsSNRVDLIED--AF--DIAFRMGSLE 153
Cdd:PRK10837   79 ----EIEQLfREDngaLRIyasSTIGNYILPAMIA----RYRRDYPQLPLELSV-GNSQDVINAvlDFrvDIGLIEGPCH 149

                         170       180
                  ....*....|....*....|.
gi 1596946267 154 DAGFIARKLLDIEMGTLASPE 174
Cdd:PRK10837  150 SPELISEPWLEDELVVFAAPD 170
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-129 2.49e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 56.75  E-value: 2.49e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  31 VSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALIAAVDDVEEVRGDIKVNCvggylgEVI 110
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFC------SVT 76

                          90       100
                  ....*....|....*....|....
gi 1596946267 111 IA-----DLVNEFMQLYPDISISL 129
Cdd:PRK11716   77 AAyshlpPILDRFRAEHPLVEIKL 100
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-74 4.04e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 56.52  E-value: 4.04e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRtTRTLRLTHAGQDLYARCEQ 74
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQ 70
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-243 5.42e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 56.18  E-value: 5.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALi 84
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  85 AAVDDVEEVRGDIKVNCvggylGEVI--IADLVNEFMQLYPdiSISLDFSSN-----RVDLIEDAFDIAFRMGSLEDAGF 157
Cdd:PRK15421   81 QACNEPQQTRLRIAIEC-----HSCIqwLTPALENFHKNWP--QVEMDFKSGvtfdpQPALQQGELDLVMTSDILPRSGL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 158 IARKLLDIEMGTLASPEY-FARKGKPNhPKDLIHHDCLTGSVRK-----WS-FQAPDDTK---KTVDvhvtgrlqckNGR 227
Cdd:PRK15421  154 HYSPMFDYEVRLVLAPDHpLAAKTRIT-PEDLASETLLIYPVQRsrldvWRhFLQPAGVSpslKSVD----------NTL 222

                         250
                  ....*....|....*.
gi 1596946267 228 VLVQGAKSGNGIIRVP 243
Cdd:PRK15421  223 LLIQMVAARMGIAALP 238
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-92 6.50e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.93  E-value: 6.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   7 LSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQALIAA 86
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82


                  ....*.
gi 1596946267  87 VDDVEE 92
Cdd:PRK09906   83 RKIVQE 88
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 117-261 1.04e-08

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 53.91  E-value: 1.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 117 EFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEyFARKGKpnHPKDLIHHDCLTg 196
Cdd:cd08484    21 EFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPE-LARRLS--EPADLANETLLR- 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1596946267 197 SVR--KWS--FQAPDDTKKTVdvhvtgrlqckNG------RVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFD 261
Cdd:cd08484    97 SYRadEWPqwFEAAGVPPPPI-----------NGpvfdssLLMVEAALQGAGVALAPPSMFSRELASGALVQPFK 160
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 16-230 1.08e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.25  E-value: 1.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  16 IARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAG--------------QDLYARCEQALDNIDQ 81
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGewfvkearsvikkmQETRRQCQQVANGWRG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  82 ALIAAVDDVeeVRGDiKVNcvggylgeVIIADlvneFMQLYPDIS--ISLD--------FSSNRVDL-------IEDAFD 144
Cdd:PRK11074   93 QLSIAVDNI--VRPD-RTR--------QLIVD----FYRHFDDVEliIRQEvfngvwdaLADGRVDIaigatraIPVGGR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 145 IAFR-MGSLEDAGFIArklldiemgtlaspeyfarkgkPNHPKDLIHHDCLTGSVRKWSFQAPDDTKKTVDVHVTGRLqc 223
Cdd:PRK11074  158 FAFRdMGMLSWACVVS----------------------SDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLL-- 213


                  ....*..
gi 1596946267 224 KNGRVLV 230
Cdd:PRK11074  214 DNQRRLV 220
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 5-129 1.36e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.97  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLG-NFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRT-TRTLRLTHAGQDLYARCEQAL---DNI 79
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLldaENL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1596946267  80 DQAliaavddVEEVRgdikvncvGGYLGEVIIA-----------DLVNEFMQLYPDISISL 129
Cdd:PRK12683   81 RRL-------AEQFA--------DRDSGHLTVAtthtqaryalpKVVRQFKEVFPKVHLAL 126
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-128 1.81e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 51.53  E-value: 1.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQA---LDNIdq 81
Cdd:PRK11013    4 VSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRI-- 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1596946267  82 alIAAVDDVEEVR-GDIKVNCVGGYlGEVIIADLVNEFMQLYPDISIS 128
Cdd:PRK11013   82 --VSAAESLREFRqGQLSIACLPVF-SQSLLPGLCQPFLARYPDVSLN 126
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 116-261 3.17e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 49.60  E-value: 3.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 116 NEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYFARKGkPNHPKDLIHHDCLT 195
Cdd:cd08481    20 PDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRA-LAAPADLAHLPLLQ 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1596946267 196 GSVRKwsfQAPDDTKKTVDVHVTGRLQcknG------RVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFD 261
Cdd:cd08481    99 QTTRP---EAWRDWFEEVGLEVPTAYR---GmrfeqfSMLAQAAVAGLGVALLPRFLIEEELARGRLVVPFN 164
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-74 4.25e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.54  E-value: 4.25e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1596946267  10 IRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRtTRTLRLTHAGQDLYARCEQ 74
Cdd:PRK03635    7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQ 70
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 117-261 5.59e-07

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


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 49.07  E-value: 5.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 117 EFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEyFARKGKpnHPKDLIHHDCLTg 196
Cdd:cd08488    21 DFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPE-LARQLR--EPADLARHTLLR- 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1596946267 197 svrkwSFQAPDDTKKTVDVHVTGRLQCKNGRV------LVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFD 261
Cdd:cd08488    97 -----SYRADEWPQWFEAAGVGHPCGLPNSIMfdsslgMMEAALQGLGVALAPPSMFSRQLASGALVQPFA 162
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 5-129 5.80e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 49.99  E-value: 5.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRsFVL-IARLG-NFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRT-TRTLRLTHAGQDLyarceqaLDNIDq 81
Cdd:PRK12682    1 MNLQQLR-FVReAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAV-------LDVIE- 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1596946267  82 ALIAAVDDVEEVRGDIKVNCVGGylgeVIIA-----------DLVNEFMQLYPDISISL 129
Cdd:PRK12682   72 RILREVGNIKRIGDDFSNQDSGT----LTIAtthtqaryvlpRVVAAFRKRYPKVNLSL 126
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
10-70 6.77e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.63  E-value: 6.77e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1596946267  10 IRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDL--YA 70
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLlpYA 68
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-144 1.52e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 48.87  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLS-DI-RSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLT-HAGQDL-YAR--------- 71
Cdd:PRK15092    9 INLDlDLlRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTeHGIQLLgYARkilrfndea 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1596946267  72 CEQAL-DNIDQAL-IAAVDDVeevrgdikvncvggylGEVIIADLVNEFMQLYPDISIslDFSSNRVDLIEDAFD 144
Cdd:PRK15092   89 CSSLMySNLQGVLtIGASDDT----------------ADTILPFLLNRVSSVYPKLAL--DVRVKRNAFMMEMLE 145
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 115-291 2.67e-06

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 46.95  E-value: 2.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 115 VNEFMQLYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEYF-ARKGKpnHPKDLIHHDC 193
Cdd:cd08483    19 LGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLgDRKVD--SLADLAGLPW 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 194 L----TGSVRKW--SFQAPDDTKKTVDVhvtgrlqcKNGRVLVQGAKSGNGIIRVPTIYCLQELNDGQLEQVFDEwvvpk 267
Cdd:cd08483    97 LqergTNEQRVWlaSMGVVPDLERGVTF--------LPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTVLFEE----- 163

                         170       180
                  ....*....|....*....|....*..
gi 1596946267 268 VDFSAIYHRDRYQP---SRIRTFIDFV 291
Cdd:cd08483   164 EEEGLGYHIVTRPGvlrPAAKAFVRWL 190
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 107-291 2.84e-06

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: 47.10  E-value: 2.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 107 GEVIIADLVNEFMQLYPDISISLDFSSNR--VDLIED-AFDIAFRMGSLEDAGFIARKLLDIEMGTLASPEY-FARKGKP 182
Cdd:cd08420    11 GEYLLPRLLARFRKRYPEVRVSLTIGNTEeiAERVLDgEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHpLAGRKEV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 183 NhPKDLIHHDCLT---GS-VR-------KWSFQAPDDTKKTVDVHVTGrlqckngrVLVQGAKSGNGIIRVPTIYCLQEL 251
Cdd:cd08420    91 T-AEELAAEPWILrepGSgTRevferalAEAGLDGLDLNIVMELGSTE--------AIKEAVEAGLGISILSRLAVRKEL 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1596946267 252 NDGQLEQVFDEWVVPKVDFSAIYHRDRYQPSRIRTFIDFV 291
Cdd:cd08420   162 ELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK12680 PRK12680
LysR family transcriptional regulator;
5-146 7.33e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 46.92  E-value: 7.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   5 INLSDIRSFVLIARLG-NFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLR-LTHAGQDLYARCEQALDNIDQA 82
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1596946267  83 LIAAVDDVEEVRGDIKVNCVGGYlGEVIIADLVNEFMQLYPDISISLDFS--SNRVDLIE--DAfDIA 146
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQ-ARFVLPPAVAQIKQAYPQVSVHLQQAaeSAALDLLGqgDA-DIA 146
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-297 2.10e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 45.43  E-value: 2.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   2 LNQINLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYARCEQALDNIDQ 81
Cdd:PRK10082    8 LHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  82 ALIAAVDDVEEVRGDIKVNCVGGY-LGEV--IIADLVNEFMqlYPDISISLDFSSNRVDLIEDAFDIAFRMGSLEDAGFI 158
Cdd:PRK10082   88 NLAELRGGSDYAQRKIKIAAAHSLsLGLLpsIISQMPPLFT--WAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFD 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267 159 ARKLLDIEMGTL-ASPEYfarkGKPNHPKDLIHHDCLTGSVRKWSFQAPDDT-KKTVDVHVTGRLQCKNGRVLVQGAKSG 236
Cdd:PRK10082  166 HIRLFESQLFPVcASDEH----GEALFNLAQPHFPLLNYSRNSYMGRLINRTlTRHSELSFSTFFVSSMSELLKQVALDG 241

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1596946267 237 NGIIRVPTIYCLQELNDGQLEQV-FDEWVVPKVDFSaiyhrdryqpSRIRTFIDFVKDRFER 297
Cdd:PRK10082  242 CGIAWLPEYAIQQEIRSGQLVVLnRDELVIPIQAYA----------YRMNTRMNPVAERFWR 293
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 6-75 3.59e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 44.64  E-value: 3.59e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   6 NLSDIRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLyarCEQA 75
Cdd:PRK11151    2 NIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLL---VDQA 68
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
6-129 3.95e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 44.58  E-value: 3.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   6 NLSDIRSFVLIARLG-NFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLR-LTHAGQ---DLYARCEQALDNID 80
Cdd:PRK12684    2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRiilASVERILQEVENLK 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1596946267  81 Q--ALIAAVDDveevrgdikvncvggylGEVIIA-----------DLVNEFMQLYPDISISL 129
Cdd:PRK12684   82 RvgKEFAAQDQ-----------------GNLTIAtthtqaryalpAAIKEFKKRYPKVRLSI 126
cbl PRK12679
HTH-type transcriptional regulator Cbl;
21-129 1.54e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.49  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  21 NFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRT-TRTLRLTHAGQDLYARCEQALdnidqaliaavDDVEEVR--GDI 97
Cdd:PRK12679   18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRgKRLLGMTEPGKALLVIAERIL-----------NEASNVRrlADL 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1596946267  98 KVNCVGGYL--------GEVIIADLVNEFMQLYPDISISL 129
Cdd:PRK12679   87 FTNDTSGVLtiatthtqARYSLPEVIKAFRELFPEVRLEL 126
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
1-91 1.69e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 41.11  E-value: 1.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267   1 MLNQINLSDIRSFVL--IARLG--NFTKAAEELDVSRSHVSRQVSSLEKQmGvtlFIRTTR--------TLRLTHAGQDL 68
Cdd:COG1846    30 ALAELGLTPAQFRVLaaLAEAGglTQSELAERLGLTKSTVSRLLDRLEEK-G---LVEREPdpedrravLVRLTEKGRAL 105

                          90       100
                  ....*....|....*....|...
gi 1596946267  69 YARCEQALDNIDQALIAAVDDVE 91
Cdd:COG1846   106 LEEARPALEALLAELLAGLSEEE 128
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
10-71 5.42e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 40.81  E-value: 5.42e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1596946267  10 IRSFVLIARLGNFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTLRLTHAGQDLYAR 71
Cdd:PRK15243    9 LKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRK 70
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
5-91 1.11e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.57  E-value: 1.11e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267    5 INLSDIRSFVLIARLG--NFTKAAEELDVSRSHVSRQVSSLEKqMGvtlFIRTTR--------TLRLTHAGQDLYARCEQ 74
Cdd:smart00347   8 LTPTQFLVLRILYEEGplSVSELAKRLGVSPSTVTRVLDRLEK-KG---LVRREPspedrrsvLVSLTEEGRELIEQLLE 83

                           90
                   ....*....|....*..
gi 1596946267   75 ALDNIDQALIAAVDDVE 91
Cdd:smart00347  84 ARSETLAELLAGLTAEE 100
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-126 6.54e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 37.57  E-value: 6.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946267  21 NFTKAAEELDVSRSHVSRQVSSLEKQMGVTLFIRTTRTL-RLTHAGQDLYArceqaldnIDQALIAAVDDVEEVRGD-IK 98
Cdd:PRK12681   18 NVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIR--------IAREILSKVESIKSVAGEhTW 89

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1596946267  99 VNCvggylGEVIIA-----------DLVNEFMQLYPDIS 126
Cdd:PRK12681   90 PDK-----GSLYIAtthtqaryalpPVIKGFIERYPRVS 123
 
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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