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Conserved domains on  [gi|1243035561|gb|ATB35632|]
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transcriptional regulator [Cystobacter fuscus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

LysR family transcriptional regulator similar to Pseudomonas aeruginosa HTH-type transcriptional regulator PtxR, which regulates the toxA (exotoxin) and regA genes; substrate binding domain-containing protein is a type 2 periplasmic binding protein (PBP2), similar to the regulatory domain of Vibrio vulnificus virulence gene regulator AphB that has been implicated in acid resistance and pathogenesis

Gene Ontology:  GO:0001216|GO:0032993|GO:0006355
PubMed:  19047729|8257110

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 ...
 103-303 1.90e-80

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: 241.96  E-value: 1.90e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAQgrHECIRVRNPftESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08422    81 LARHGTPQTPEDLAR--HRCLGYRLP--GRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
20-74 2.76e-20

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.43  E-value: 2.76e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGR 74
Cdd:pfam00126   6 LFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 103-303 1.90e-80

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: 241.96  E-value: 1.90e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAQgrHECIRVRNPftESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08422    81 LARHGTPQTPEDLAR--HRCLGYRLP--GRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
20-308 2.95e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 200.48  E-value: 2.95e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:COG0583     8 AFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 100 AVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDR---IGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLT 176
Cdd:COG0583    88 GPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVL 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 177 CASPEYIARHGRPkhpselaqgrhecirvrnpftesyfewefqrgeeiipvnvqgrlVVNDSGSLIGAMLSGHGIGQPFE 256
Cdd:COG0583   168 VASPDHPLARRAP--------------------------------------------LVNSLEALLAAVAAGLGIALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1243035561 257 FSVRDLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFLLEIAK 308
Cdd:COG0583   204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
15-305 1.04e-44

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 154.15  E-value: 1.04e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  15 LGGMGVLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATV 94
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  95 SDAAGAVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRV 174
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPM 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 175 LTCASPEYIARHGRPKHPSELAQGRHECIRVRnpfTESYFEWEFQRGE--EIIPvnvQGRLVVNDSGSLIGAMLSGHGIG 252
Cdd:PRK10632  164 VVCAAKSYLAQYGTPEKPADLSSHSWLEYSVR---PDNEFELIAPEGIstRLIP---QGRFVTNDPQTLVRWLTAGAGIA 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1243035561 253 QPFEFSVRDLLESGRLVKLLPTW-SDERyPVY-VYHRSRELPaARVRAFIDFLLE 305
Cdd:PRK10632  238 YVPLMWVIDEINRGELEILFPRYqSDPR-PVYaLYTEKDKLP-LKVQVCINYLTD 290
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-305 3.22e-31

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: 115.85  E-value: 3.22e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 102 RGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVV--RDRIGDLVAEG-LDMAVRFGEAEPSGLISRQLARSRVLTCA 178
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 179 SPEYIARHGRPKHPSELAqgRHECIRVRnpfTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFS 258
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLA--DEPLILLP---PGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1243035561 259 VRDLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFLLE 305
Cdd:pfam03466 156 VARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 24-306 9.19e-26

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: 103.85  E-value: 9.19e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  24 VVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRG 103
Cdd:NF040786   12 VAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRD--RIGDLVAEG-LDMAVRFGEAEPSGLISRQLARSR--VLTCA 178
Cdd:NF040786   92 VLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGFTGTKLEKKRLVYTPFYKDRlvLITPN 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 179 SPEYIARHGRPKHPSELaQGRHECIRVRNPFTESYFEWEFQR-GEEIIPVNVQgrLVVNDSGSLIGAMLSGHGIGQPFEF 257
Cdd:NF040786  172 GTEKYRMLKEEISISEL-QKEPFIMREEGSGTRKEAEKALKSlGISLEDLNVV--ASLGSTEAIKQSVEAGLGISVISEL 248

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1243035561 258 SVRDLLESGRlVKLLPTWSDE--RYPVYVYHRSRELPAArVRAFIDFLLEI 306
Cdd:NF040786  249 AAEKEVERGR-VLIFPIPGLPknRDFYLVYNKNRQLSPT-AEAFLQFVKER 297
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
20-74 2.76e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.43  E-value: 2.76e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGR 74
Cdd:pfam00126   6 LFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 21-186 7.73e-19

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 84.58  E-value: 7.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTaRAVSLTDEGR---RFYEQVAPLLAgieDAAATVSDA 97
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQrllRHARQVRLLEA---ELLAELPGL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  98 AGAVRGLLR--VNVDSAfgHNVLAPRLGEFLARHPALsVELVVRD--RIGDLVAEGLDMAVRFGEAEP-SGLISRQLARS 172
Cdd:TIGR03298  85 APGAPTRLTiaVNADSL--ATWFLPALAPVLAREGVL-LDLVVEDqdHTAELLRSGEVLGAVTTEAKPvPGCRVVPLGAM 161

                         170
                  ....*....|....
gi 1243035561 173 RVLTCASPEYIARH 186
Cdd:TIGR03298 162 RYLAVASPAFAARY 175
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 20-110 4.08e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.49  E-value: 4.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:PRK11074    9 VVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVAN 88

                          90
                  ....*....|.
gi 1243035561 100 AVRGLLRVNVD 110
Cdd:PRK11074   89 GWRGQLSIAVD 99
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 21-90 1.40e-08

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.13  E-value: 1.40e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLaGIEDA 90
Cdd:NF041036    9 LVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL-DIEDS 77
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
34-91 3.66e-05

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 43.03  E-value: 3.66e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1243035561  34 AESLGMTQSGVSRAVARLEQRvG-VRLF----DRTARAVSLTDEGRRFYEQVAPLLAGIEDAA 91
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLEEK-GlVEREpdpeDRRAVLVRLTEKGRALLEEARPALEALLAEL 120
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
34-90 8.74e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.96  E-value: 8.74e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1243035561   34 AESLGMTQSGVSRAVARLEQRVGVRLF----DRTARAVSLTDEGRRFYEQVAPLLAGIEDA 90
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLEKKGLVRREpspeDRRSVLVSLTEEGRELIEQLLEARSETLAE 91
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 103-303 1.90e-80

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: 241.96  E-value: 1.90e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAQgrHECIRVRNPftESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08422    81 LARHGTPQTPEDLAR--HRCLGYRLP--GRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08422   157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-306 6.89e-66

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: 205.05  E-value: 6.89e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAQgrHECIRVRNPFTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08472    81 LARHGTPRHPEDLER--HRAVGYFSARTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPH 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1243035561 263 LESGRLVKLLPTWSDERYPVY-VYHRSRELPaARVRAFIDFLLEI 306
Cdd:cd08472   159 LASGRLVEVLPDWRPPPLPVSlLYPHRRHLS-PRVRVFVDWVAEL 202
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
20-308 2.95e-63

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 200.48  E-value: 2.95e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:COG0583     8 AFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 100 AVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDR---IGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLT 176
Cdd:COG0583    88 GPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVL 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 177 CASPEYIARHGRPkhpselaqgrhecirvrnpftesyfewefqrgeeiipvnvqgrlVVNDSGSLIGAMLSGHGIGQPFE 256
Cdd:COG0583   168 VASPDHPLARRAP--------------------------------------------LVNSLEALLAAVAAGLGIALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1243035561 257 FSVRDLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFLLEIAK 308
Cdd:COG0583   204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-303 9.04e-62

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: 194.60  E-value: 9.04e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 102 RGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLA-RSRVLTCASP 180
Cdd:cd08474     2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGpPLRMAVVASP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 181 EYIARHGRPKHPSELAQgrHECIRVRNPFTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVR 260
Cdd:cd08474    82 AYLARHGTPEHPRDLLN--HRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1243035561 261 DLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08474   160 EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 1.89e-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: 1.89e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAqgRHECIRVRNPFTESyfEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIG-QPFEFsVRD 261
Cdd:cd08477    81 LARHGTPTTPEDLA--RHECLGFSYWRARN--RWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVlQPEAL-LAE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1243035561 262 LLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08477   156 DLASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 4.78e-53

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: 172.32  E-value: 4.78e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAqgRHECIRVRNPFteSYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08471    81 LARHGTPKHPDDLA--DHDCIAFTGLS--PAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08471   157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFA 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 1.23e-52

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: 171.24  E-value: 1.23e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAqgRHECIRVRNPfTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08479    81 LERHGAPASPEDLA--RHDCLVIREN-DEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPY 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08479   158 LRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 3.88e-46

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: 154.39  E-value: 3.88e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAqgRHECIRVRNPFtesyfeWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08470    81 LERHGTPHSLADLD--RHNCLLGTSDH------WRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEH 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1243035561 263 LESGRLVKLLPTWSDERYPVY-VYHRSRELPaARVRAFIDFL 303
Cdd:cd08470   153 LAAGRLVPVLEDYRPPDEGIWaLYPHNRHLS-PKVRLLVDYL 193
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 3.75e-45

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: 152.01  E-value: 3.75e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSafGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08476     1 GRLRVSLPL--VGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAQgrHECIRVRNPFTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08476    79 LARHGTPETPADLAE--HACLRYRFPTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08476   157 LADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
15-305 1.04e-44

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 154.15  E-value: 1.04e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  15 LGGMGVLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATV 94
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  95 SDAAGAVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRV 174
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPM 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 175 LTCASPEYIARHGRPKHPSELAQGRHECIRVRnpfTESYFEWEFQRGE--EIIPvnvQGRLVVNDSGSLIGAMLSGHGIG 252
Cdd:PRK10632  164 VVCAAKSYLAQYGTPEKPADLSSHSWLEYSVR---PDNEFELIAPEGIstRLIP---QGRFVTNDPQTLVRWLTAGAGIA 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1243035561 253 QPFEFSVRDLLESGRLVKLLPTW-SDERyPVY-VYHRSRELPaARVRAFIDFLLE 305
Cdd:PRK10632  238 YVPLMWVIDEINRGELEILFPRYqSDPR-PVYaLYTEKDKLP-LKVQVCINYLTD 290
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 6.03e-44

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: 149.02  E-value: 6.03e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARHGRPKHPSELAqgRHECIRVRnpFTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDL 262
Cdd:cd08480    81 LARHGTPLTPQDLA--RHNCLGFN--FRRALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADD 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1243035561 263 LESGRLVKLL-PTWSDERYPVY-VYHRSRELPaARVRAFIDFL 303
Cdd:cd08480   157 IAAGRLVPVLeEYNPGDREPIHaVYVGGGRLP-ARVRAFLDFL 198
PRK09801 PRK09801
LysR family transcriptional regulator;
20-295 1.30e-43

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 151.34  E-value: 1.30e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:PRK09801   13 VLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKT 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 100 AVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCAS 179
Cdd:PRK09801   93 RPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCAA 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 180 PEYIARHGRPKHPSELAqgRHECIrVRNPFTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSV 259
Cdd:PRK09801  173 PEYLQKYPQPQSLQELS--RHDCL-VTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDV 249

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1243035561 260 RDLLESGRLVKLLP-------TWSDERYPVYvyhRSRELPAAR 295
Cdd:PRK09801  250 LPFLESGKLVQVLPeyaqsanIWAVYREPLY---RSMKLRVCV 289
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-303 5.70e-43

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: 146.16  E-value: 5.70e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGE-AEPSGLISRQLARSRVLTCASPE 181
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGElADSTGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 182 YIARHGRPKHPSELAQgrHECI----RVRNPftesyfEWEFQR-GEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFE 256
Cdd:cd08475    81 YLARHGTPRTLEDLAE--HQCIaygrGGQPL------PWRLADeQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPT 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1243035561 257 FSVRDLLESGRLVKLLPTWSDERYPVY-VYHRSRELPaARVRAFIDFL 303
Cdd:cd08475   153 WLVADHLQRGELVEVLPELAPEGLPIHaVWPRTRHLP-PKVRAAVDAL 199
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 24-305 1.80e-39

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 140.51  E-value: 1.80e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  24 VVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRG 103
Cdd:PRK14997   13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEA--EPSGLISRQLARSRVLTCASPE 181
Cdd:PRK14997   93 IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRpfEDSDLVMRVLADRGHRLFASPD 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 182 YIARHGRPKHPSEL--------AQGRHEcirvrnpftesyFEWE-FQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIG 252
Cdd:PRK14997  173 LIARMGIPSAPAELshwpglslASGKHI------------HRWElYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLV 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1243035561 253 QPFEFSVRDLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFLLE 305
Cdd:PRK14997  241 QLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTE 293
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 29-308 3.00e-37

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 134.20  E-value: 3.00e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  29 SFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIedAAATVSDAAGAVRGLLRVN 108
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL--AEATRKLRARSAKGALTVS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 109 VDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEYIARHGR 188
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKP 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 189 PKHPSELAqgRHECIRVRNPftESYFEWEFQRGeeIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDLLESGRL 268
Cdd:PRK11139  180 LKTPEDLA--RHTLLHDDSR--EDWRAWFRAAG--LDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRL 253

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1243035561 269 VKLLPT--WSDERYPVyVYHRSR-ELPaaRVRAFIDFLL-EIAK 308
Cdd:PRK11139  254 VCPFDTvlPSPNAFYL-VCPDSQaELP--KVAAFRQWLLaEAAQ 294
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-303 1.63e-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 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: 129.60  E-value: 1.63e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 102 RGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMA--VRFGEAEPSGLISRQLARSRVLTCAS 179
Cdd:cd08473     2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVAlrVRFPPLEDSSLVMRVLGQSRQRLVAS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 180 PEYIARHGRPKHPSELAqgRHECIRVRNPFTESyfEWEFQRGE-EIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFS 258
Cdd:cd08473    82 PALLARLGRPRSPEDLA--GLPTLSLGDVDGRH--SWRLEGPDgESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1243035561 259 VRDLLESGRLVKLLPTWSDERYPVYVYHRSRE--LPAarVRAFIDFL 303
Cdd:cd08473   158 CREALRAGRLVRVLPDWTPPRGIVHAVFPSRRglLPA--VRALIDFL 202
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 102-303 6.07e-34

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: 122.83  E-value: 6.07e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 102 RGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPE 181
Cdd:cd08478     2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 182 YIARHGRPKHPSELAQgrHECIRVRNPftESYFEWEFQRGEEiIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRD 261
Cdd:cd08478    82 YLARHGTPQSIEDLAQ--HQLLGFTEP--ASLNTWPIKDADG-NLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDK 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1243035561 262 LLESGRLVKLL-PTWSDERYPVY-VYHRSRElPAARVRAFIDFL 303
Cdd:cd08478   157 DIAEGRLIPLFaEQTSDVRQPINaVYYRNTA-LSLRIRCFIDFL 199
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 105-303 2.08e-31

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: 116.14  E-value: 2.08e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 105 LRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEYIA 184
Cdd:cd08432     2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 185 RHGRPKhPSELAqgRHECIRVRnpfTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGI--GQPfeFSVRDL 262
Cdd:cd08432    82 GLPLLS-PADLA--RHTLLHDA---TRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGValAPR--ALVADD 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1243035561 263 LESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08432   154 LAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-308 2.75e-31

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 118.95  E-value: 2.75e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  11 DGKLLGGMGVLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYeqvAPLLAGIEDA 90
Cdd:PRK10086   12 NGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF---WALKSSLDTL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  91 AATVSDAAGA-VRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQL 169
Cdd:PRK10086   89 NQEILDIKNQeLSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFL 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 170 ARSRVLTCASPEYIARHGRPKHPSELAQgrheCIRV-------RNPFTESYFEWEFQRGEEIIPvnvQGRLVVNDSGSL- 241
Cdd:PRK10086  169 MDEEILPVCSPEYAERHALTGNPDNLRH----CTLLhdrqawsNDSGTDEWHSWAQHFGVNLLP---PSSGIGFDRSDLa 241

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1243035561 242 -IGAMlsGH-GIGQPFEFSVRDLLESGRLVKLLPTW---SDERYpvYVYHRSRELPaARVRAFIDFLLEIAK 308
Cdd:PRK10086  242 vIAAM--NHiGVAMGRKRLVQKRLASGELVAPFGDMevkCHQHY--YVTTLPGRQW-PKIEAFIDWLKEQVK 308
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-305 3.22e-31

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: 115.85  E-value: 3.22e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 102 RGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVV--RDRIGDLVAEG-LDMAVRFGEAEPSGLISRQLARSRVLTCA 178
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 179 SPEYIARHGRPKHPSELAqgRHECIRVRnpfTESYFEWEFQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFS 258
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLA--DEPLILLP---PGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1243035561 259 VRDLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFLLE 305
Cdd:pfam03466 156 VARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 24-306 9.19e-26

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: 103.85  E-value: 9.19e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  24 VVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRG 103
Cdd:NF040786   12 VAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRD--RIGDLVAEG-LDMAVRFGEAEPSGLISRQLARSR--VLTCA 178
Cdd:NF040786   92 VLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGFTGTKLEKKRLVYTPFYKDRlvLITPN 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 179 SPEYIARHGRPKHPSELaQGRHECIRVRNPFTESYFEWEFQR-GEEIIPVNVQgrLVVNDSGSLIGAMLSGHGIGQPFEF 257
Cdd:NF040786  172 GTEKYRMLKEEISISEL-QKEPFIMREEGSGTRKEAEKALKSlGISLEDLNVV--ASLGSTEAIKQSVEAGLGISVISEL 248

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1243035561 258 SVRDLLESGRlVKLLPTWSDE--RYPVYVYHRSRELPAArVRAFIDFLLEI 306
Cdd:NF040786  249 AAEKEVERGR-VLIFPIPGLPknRDFYLVYNKNRQLSPT-AEAFLQFVKER 297
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
20-74 2.76e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.43  E-value: 2.76e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGR 74
Cdd:pfam00126   6 LFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 21-186 7.73e-19

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 84.58  E-value: 7.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTaRAVSLTDEGR---RFYEQVAPLLAgieDAAATVSDA 97
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQrllRHARQVRLLEA---ELLAELPGL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  98 AGAVRGLLR--VNVDSAfgHNVLAPRLGEFLARHPALsVELVVRD--RIGDLVAEGLDMAVRFGEAEP-SGLISRQLARS 172
Cdd:TIGR03298  85 APGAPTRLTiaVNADSL--ATWFLPALAPVLAREGVL-LDLVVEDqdHTAELLRSGEVLGAVTTEAKPvPGCRVVPLGAM 161

                         170
                  ....*....|....
gi 1243035561 173 RVLTCASPEYIARH 186
Cdd:TIGR03298 162 RYLAVASPAFAARY 175
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 21-159 1.28e-17

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 81.16  E-value: 1.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGA 100
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1243035561 101 VRGLLRVNVDSAFGHNVLAPRLGEFLARHP--ALSVELVVRDRIGDLVAEG-LDMAVRFGEA 159
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPgiTLTIREMSQERIEALLADDeLDVGIAFAPV 150
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 104-303 7.03e-17

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: 77.34  E-value: 7.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEYI 183
Cdd:cd08481     1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 184 ARHGrPKHPSELAQGR--HECIRvrnPftESYFEWeFQRGEEIIPVNVQGRLvVNDSGSLIGAMLSGHGIGQPFEFSVRD 261
Cdd:cd08481    81 AGRA-LAAPADLAHLPllQQTTR---P--EAWRDW-FEEVGLEVPTAYRGMR-FEQFSMLAQAAVAGLGVALLPRFLIEE 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1243035561 262 LLESGRLVKL--LPTWSDERYPVYVYHRSRELPAarVRAFIDFL 303
Cdd:cd08481   153 ELARGRLVVPfnLPLTSDKAYYLVYPEDKAESPP--VQAFRDWL 194
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
21-273 1.35e-16

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 78.28  E-value: 1.35e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTaRAVSLTDEGR---RFYEQVAPLlagiEDAAATVSDA 97
Cdd:PRK03635   10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQrllRHARQVRLL----EAELLGELPA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  98 AGAVRGLLR--VNVDSafghnvLA----PRLGEFLARHPALsVELVVRD--RIGDLVAEGLDMAVRFGEAEP-SGLISRQ 168
Cdd:PRK03635   85 LDGTPLTLSiaVNADS------LAtwflPALAPVLARSGVL-LDLVVEDqdHTAELLRRGEVVGAVTTEPQPvQGCRVDP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 169 LARSRVLTCASPEYIARHgrpkhpseLAQG-RHECIRvRNPFT---------ESYFEWEFQRGEEIIPVNvqgrlVVNDS 238
Cdd:PRK03635  158 LGAMRYLAVASPAFAARY--------FPDGvTAEALA-KAPAVvfnrkddlqDRFLRQAFGLPPGSVPCH-----YVPSS 223

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1243035561 239 GSLIGAMLSGHGIGQPFEFSVRDLLESGRLVKLLP 273
Cdd:PRK03635  224 EAFVRAALAGLGWGMIPELQIEPELASGELVDLTP 258
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
21-186 7.38e-15

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 73.47  E-value: 7.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTaRAVSLTDEGRRFY---EQV----APLLAGIEDAaat 93
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLrhlRQValleADLLSTLPAE--- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  94 vsdAAGAVRGLLRVNVDSafghnvLA----PRLGEFLARHPALsVELVV--RDRIGDLVAEGLDMAVRFGEAEP-SGLIS 166
Cdd:PRK13348   86 ---RGSPPTLAIAVNADS------LAtwflPALAAVLAGERIL-LELIVddQDHTFALLERGEVVGCVSTQPKPmRGCLA 155

                         170       180
                  ....*....|....*....|
gi 1243035561 167 RQLARSRVLTCASPEYIARH 186
Cdd:PRK13348  156 EPLGTMRYRCVASPAFAARY 175
PRK09986 PRK09986
LysR family transcriptional regulator;
23-220 2.15e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 72.06  E-value: 2.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  23 AVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVR 102
Cdd:PRK09986   17 AVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 103 GLLRVN-VDSAFGHNVLaPRLGEFLARHPALSV---ELVVRDRIGDLVAEGLDMAV-RFGEAEPS-GLISRQLARSRVLT 176
Cdd:PRK09986   97 GRIEIGiVGTALWGRLR-PAMRHFLKENPNVEWllrELSPSMQMAALERRELDAGIwRMADLEPNpGFTSRRLHESAFAV 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1243035561 177 cASPEYIARHGRPKHPseLAQGRHECIrVRNPFTESYFEWEFQR 220
Cdd:PRK09986  176 -AVPEEHPLASRSSVP--LKALRNEYF-ITLPFVHSDWGKFLQR 215
rbcR CHL00180
LysR transcriptional regulator; Provisional
 20-158 1.47e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 69.66  E-value: 1.47e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:CHL00180   12 ILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKN 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1243035561 100 AVRGLLRVNVDSAFGhNVLAPRL-GEFLARHPALSVELVVRD--RIGDLVAEG-LDMAVRFGE 158
Cdd:CHL00180   92 LQRGTLIIGASQTTG-TYLMPRLiGLFRQRYPQINVQLQVHStrRIAWNVANGqIDIAIVGGE 153
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 105-303 3.23e-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: 3.23e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 105 LRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVR--DRIGDLVAEG-LDMAVRFGEAEPSGLISRQLARSRVLTCASPE 181
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGgsSELLEALLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 182 YIARHGRPKHPSELAqgRHECI-RVRNPFTESYFEWEFQrgEEIIPVNVqgRLVVNDSGSLIGAMLSGHGIGqpfeF--- 257
Cdd:cd05466    82 HPLAKRKSVTLADLA--DEPLIlFERGSGLRRLLDRAFA--EAGFTPNI--ALEVDSLEAIKALVAAGLGIA----Llpe 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1243035561 258 SVRDLLESGRLVKLLPTWSDERYPVYVYHRSRELPAARVRAFIDFL 303
Cdd:cd05466   152 SAVEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 20-157 3.65e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 65.48  E-value: 3.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLagieDAAATVSDAAG 99
Cdd:PRK10837   10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL----EQAVEIEQLFR 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1243035561 100 AVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIgDLVAEGLDMAVRFG 157
Cdd:PRK10837   86 EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQ-DVINAVLDFRVDIG 142
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 23-137 4.06e-12

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 65.56  E-value: 4.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  23 AVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVR 102
Cdd:PRK09906   11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQEDR 90

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1243035561 103 GLLRVNVDSAfGHNVLAPRLGEFLARHPALSVELV 137
Cdd:PRK09906   91 QLTIGFVPSA-EVNLLPKVLPMFRLRHPDTLIELV 124
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 105-303 4.43e-12

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: 63.90  E-value: 4.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 105 LRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEYIA 184
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 185 rhGRPK-HPSELAqgRHECIRVRNpfTESYFEWEFQRGeeIIPVNVQGRLVVNDsGSLIGAMLSGHGIG-QPFEFSVRDl 262
Cdd:cd08483    82 --DRKVdSLADLA--GLPWLQERG--TNEQRVWLASMG--VVPDLERGVTFLPG-QLVLEAARAGLGLSiQARALVEPD- 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1243035561 263 LESGRLVKLLptwsDERYPVYVYH--RSRELPAARVRAFIDFL 303
Cdd:cd08483   152 IAAGRLTVLF----EEEEEGLGYHivTRPGVLRPAAKAFVRWL 190
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 105-303 6.84e-12

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 63.28  E-value: 6.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 105 LRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRD--RIGDLVAEG-LDMAVRFGEAEPSGLISRQLARSRVLTCASPE 181
Cdd:cd08420     2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNteEIAERVLDGeIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 182 YIARHGRPKHPSELAQGrhecirvrnPF--------TESYFEWEFQR-GEEIIPVNVqgRLVVNDSGSLIGAMLSGHGIG 252
Cdd:cd08420    82 HPLAGRKEVTAEELAAE---------PWilrepgsgTREVFERALAEaGLDGLDLNI--VMELGSTEAIKEAVEAGLGIS 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1243035561 253 QPFEFSVRDLLESGRLVKL-LPTWSDERYPVYVYHRSRELPAArVRAFIDFL 303
Cdd:cd08420   151 ILSRLAVRKELELGRLVALpVEGLRLTRPFSLIYHKDKYLSPA-AEAFLEFL 201
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 104-274 1.76e-11

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: 62.16  E-value: 1.76e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEyI 183
Cdd:cd08488     1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPE-L 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 184 ARHGRpkHPSELAqgRHECIRvrnpfteSYF--EWE--FQRGEEIIPVNVQGRLVVNDSGSLIGAMLSGHGI--GQPFEF 257
Cdd:cd08488    80 ARQLR--EPADLA--RHTLLR-------SYRadEWPqwFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGValAPPSMF 148

                         170
                  ....*....|....*..
gi 1243035561 258 SvRDLLeSGRLVKLLPT 274
Cdd:cd08488   149 S-RQLA-SGALVQPFAT 163
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 104-274 2.87e-11

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: 61.23  E-value: 2.87e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEyI 183
Cdd:cd08484     1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPE-L 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 184 ARhgRPKHPSELAqgRHECIRvrnpfteSYF--EWE--FQR-GEEIIPVNvqgRLVVNDSGSLIGAMLSGHGIG--QPFE 256
Cdd:cd08484    80 AR--RLSEPADLA--NETLLR-------SYRadEWPqwFEAaGVPPPPIN---GPVFDSSLLMVEAALQGAGVAlaPPSM 145

                         170
                  ....*....|....*...
gi 1243035561 257 FSVRdlLESGRLVKLLPT 274
Cdd:cd08484   146 FSRE--LASGALVQPFKI 161
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 24-171 3.67e-11

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 62.78  E-value: 3.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  24 VVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRG 103
Cdd:PRK11233   12 IVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSG 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1243035561 104 llRVNVDSAFG---HNVLAPRLGEFLARHPALSVELvvRDRIG----DLVAEG-LDMAVRFGEAEPSGLISRQLAR 171
Cdd:PRK11233   92 --QVSIGLAPGtaaSSLTMPLLQAVRAEFPGIVLYL--HENSGatlnEKLMNGqLDMAVIYEHSPVAGLSSQPLLK 163
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 20-137 2.70e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 60.01  E-value: 2.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAAtvsdAAG 99
Cdd:PRK11013   11 IFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVS----AAE 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1243035561 100 AVR----GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELV 137
Cdd:PRK11013   87 SLRefrqGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIV 128
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 23-189 1.24e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 58.12  E-value: 1.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  23 AVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATV--SDaaga 100
Cdd:PRK15092   21 AVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLmySN---- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 101 VRGLLRVNV--DSAfghNVLAPRLgefLAR----HPALSVELVVRDR--IGDLVAEG-LDMAVRfgEAEPSGLISRQLAR 171
Cdd:PRK15092   97 LQGVLTIGAsdDTA---DTILPFL---LNRvssvYPKLALDVRVKRNafMMEMLESQeVDLAVT--THRPSSFPALNLRT 168

                         170
                  ....*....|....*...
gi 1243035561 172 SRVLTCASPEYIARHGRP 189
Cdd:PRK15092  169 SPTLWYCAAEYVLQKGEP 186
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 20-110 4.08e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.49  E-value: 4.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:PRK11074    9 VVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVAN 88

                          90
                  ....*....|.
gi 1243035561 100 AVRGLLRVNVD 110
Cdd:PRK11074   89 GWRGQLSIAVD 99
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
23-88 8.04e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.58  E-value: 8.04e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1243035561  23 AVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIE 88
Cdd:PRK10094   12 AVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
29-271 9.90e-09

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 55.45  E-value: 9.90e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  29 SFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSdaAGAVRGLLRVN 108
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELR--GGSDYAQRKIK 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 109 VDSAfgHNVLAPRLGEFLARHPAL---SVELVVRDRIGDLVAEGL-DMAVRFGEAE----PSGLIsrQLARSRVL-TCAS 179
Cdd:PRK10082  105 IAAA--HSLSLGLLPSIISQMPPLftwAIEAIDVDEAVDKLREGQsDCIFSFHDEDlleaPFDHI--RLFESQLFpVCAS 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 180 PEyiarHGRPKHpsELAQGRHECIRV-RNPFTESYFEWEFQRGEEIipvNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFS 258
Cdd:PRK10082  181 DE----HGEALF--NLAQPHFPLLNYsRNSYMGRLINRTLTRHSEL---SFSTFFVSSMSELLKQVALDGCGIAWLPEYA 251

                         250
                  ....*....|...
gi 1243035561 259 VRDLLESGRLVKL 271
Cdd:PRK10082  252 IQQEIRSGQLVVL 264
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 21-90 1.40e-08

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.13  E-value: 1.40e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLaGIEDA 90
Cdd:NF041036    9 LVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL-DIEDS 77
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 118-303 2.11e-08

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


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 53.17  E-value: 2.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 118 LAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGEAE-PSGLISRQLARSRVLTCASPEYIAR-HGRPKHPSEL 195
Cdd:cd08482    15 LIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFPERVGPVCSPSLAPTvPLRQAPAAAL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 196 AQGRHECIRVRnpfTESYFEWEFQRGeeIIPVNVQGRLVVNDSGSLIGAMLSGHGIGQPFEFSVRDLLESGRLVKLLPTW 275
Cdd:cd08482    95 LGAPLLHTRSR---PQAWPDWAAAQG--LAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLVAPWGFI 169

                         170       180
                  ....*....|....*....|....*...
gi 1243035561 276 SDERYpvYVYHRSRELPAARVRAFIDFL 303
Cdd:cd08482   170 ETGSH--YVLLRPARLRDSRAGALADWL 195
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 104-270 3.22e-08

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: 52.55  E-value: 3.22e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 104 LLRVNVDSAFGHNVLAPRLGEFLARHPALSVELVVRDRIGDLVAEGLDMAVRFGE-AEPSGLISRQLARSRVLTCaSPEy 182
Cdd:cd08487     1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEgLWPATHNERLLDAPLSVLC-SPE- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 IARhgRPKHPSELAqgrHECIrVRNPFTESYFEWeFQRGeEIIPVNVQGRlVVNDSGSLIGAMLSGHGIG-QPFEFSVRD 261
Cdd:cd08487    79 IAK--RLSHPADLI---NETL-LRSYRTDEWLQW-FEAA-NMPPIKIRGP-VFDSSRLMVEAAMQGAGVAlAPAKMFSRE 149


                  ....*....
gi 1243035561 262 lLESGRLVK 270
Cdd:cd08487   150 -IENGQLVQ 157
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
39-142 1.22e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 51.74  E-value: 1.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  39 MTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRGLLRV--NVDSAFGHn 116
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcSVTAAYSH- 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1243035561 117 vLAPRLGEFLARHP-----------ALSVELVVRDRI 142
Cdd:PRK11716   82 -LPPILDRFRAEHPlveiklttgdaADAVEKVQSGEA 117
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
21-136 2.71e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 51.17  E-value: 2.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAga 100
Cdd:PRK15421   10 LQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQ-- 87

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1243035561 101 vRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVEL 136
Cdd:PRK15421   88 -QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDF 122
PRK10341 PRK10341
transcriptional regulator TdcA;
20-118 1.10e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 49.48  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  20 VLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAG 99
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSS 93

                          90
                  ....*....|....*....
gi 1243035561 100 avrgllRVNVDSAFGHNVL 118
Cdd:PRK10341   94 ------EAVVDVSFGFPSL 106
PRK09791 PRK09791
LysR family transcriptional regulator;
23-137 1.92e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 48.60  E-value: 1.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  23 AVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVR 102
Cdd:PRK09791   15 EVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQLA 94

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1243035561 103 GLLRVNVDSAFGHNVLAPRLGEFLARHPALSVELV 137
Cdd:PRK09791   95 GQINIGMGASIARSLMPAVISRFHQQHPQVKVRIM 129
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
30-75 9.95e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 46.16  E-value: 9.95e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1243035561  30 FIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRR 75
Cdd:PRK03601   18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGER 63
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
33-149 2.43e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 45.35  E-value: 2.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  33 AAESLGMTQSGVSRAVARLEQRVGVRLFDRTA-RAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRGLLRVnvds 111
Cdd:PRK12684   22 AAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTI---- 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1243035561 112 AFGHN----VLAPRLGEFLARHPalSVELVVRD----RIGDLVAEG 149
Cdd:PRK12684   98 ATTHTqaryALPAAIKEFKKRYP--KVRLSILQgsptQIAEMVLHG 141
leuO PRK09508
leucine transcriptional activator; Reviewed
 10-69 2.77e-05

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 45.01  E-value: 2.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1243035561  10 VDGKLLGgmgVLAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDR-------TARAVSL 69
Cdd:PRK09508   22 VDLNLLT---VFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRygrgiqpTARARQL 85
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
34-91 3.66e-05

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 43.03  E-value: 3.66e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1243035561  34 AESLGMTQSGVSRAVARLEQRvG-VRLF----DRTARAVSLTDEGRRFYEQVAPLLAGIEDAA 91
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLEEK-GlVEREpdpeDRRAVLVRLTEKGRALLEEARPALEALLAEL 120
PRK12680 PRK12680
LysR family transcriptional regulator;
21-175 8.72e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 43.46  E-value: 8.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  21 LAAVVDAGSFIR-AAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAV-SLTDEGRRFYEQVAPLLAGIEDAAATVSDAA 98
Cdd:PRK12680    9 LVAIADAELNITlAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  99 GAVRGLLRVNVDSAFGHNVLAPRLGEFLARHPALSVEL--VVRDRIGDLVAEG-LDMA-VRFGEAEPSGLISRQLARSRV 174
Cdd:PRK12680   89 RESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLqqAAESAALDLLGQGdADIAiVSTAGGEPSAGIAVPLYRWRR 168


                  .
gi 1243035561 175 L 175
Cdd:PRK12680  169 L 169
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
34-90 8.74e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.96  E-value: 8.74e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1243035561   34 AESLGMTQSGVSRAVARLEQRVGVRLF----DRTARAVSLTDEGRRFYEQVAPLLAGIEDA 90
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLEKKGLVRREpspeDRRSVLVSLTEEGRELIEQLLEARSETLAE 91
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 21-79 8.76e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 40.40  E-value: 8.76e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1243035561  21 LAAVVDAGSFIRAAESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYEQ 79
Cdd:PRK11151    9 LVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQ 67
PBP2_IciA_ArgP cd08428
The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), ...
 107-287 9.68e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176119 [Multi-domain]  Cd Length: 195  Bit Score: 39.54  E-value: 9.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 107 VNVDSafghnvLA----PRLGEFLARHPALsVELVVRD--RIGDLVAEGLDMAVRFGEAEP-SGLISRQLARSRVLTCAS 179
Cdd:cd08428     6 VNADS------LAtwflPALAPVLKRERIL-LDLIVDDedRTHDLLRDGEVVGCISTQAQPmQGCRSDYLGSMDYLLVAS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 180 PEYIARHGrP---------KHPSeLAQGRHEciRVRNPFTESYFewefqrgeEIIPVNVQgRLVVNDSGSLIGAMLSGHG 250
Cdd:cd08428    79 PDFAARYF-PngltreallKAPA-VAFNRKD--DLHQSFLQQHF--------GLPPGSYP-CHYVPSSEAFVDLAAQGLA 145

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1243035561 251 IGQPFEFSVRDLLESGRLVKLLPTWSdERYPVYvYHR 287
Cdd:cd08428   146 YGMIPELQIEPELASGELIDLAPGHL-LRVTLY-WHR 180
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 33-200 1.58e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 39.59  E-value: 1.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  33 AAESLGMTQSGVSRAVARLEQRVGVRLFDRTA-RAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRGLLRVNVDS 111
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTH 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 112 AFGHNVLAPRLGEFLARHPalSVELVVRDRIGDLVAEgldMAVRfGEAEpSGLISRQLARSRVLTCAsPEYIARHG---R 188
Cdd:PRK12682  102 TQARYVLPRVVAAFRKRYP--KVNLSLHQGSPDEIAR---MVIS-GEAD-IGIATESLADDPDLATL-PCYDWQHAvivP 173

                         170
                  ....*....|..
gi 1243035561 189 PKHPseLAQGRH 200
Cdd:PRK12682  174 PDHP--LAQEER 183
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 33-136 2.25e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 39.26  E-value: 2.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561  33 AAESLGMTQSGVSRAVARLEQRVGVRLFDRTA-RAVSLTDEGRRFYEQVAPLLAGIEDAAATVSDAAGAVRGLLRVNVDS 111
Cdd:PRK12683   22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTH 101

                          90       100
                  ....*....|....*....|....*
gi 1243035561 112 AFGHNVLAPRLGEFLARHPALSVEL 136
Cdd:PRK12683  102 TQARYALPKVVRQFKEVFPKVHLAL 126
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
34-78 3.59e-03

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 38.66  E-value: 3.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1243035561  34 AESLGMTQSGVSRAVARLEQRVGVRLFDRTARAVSLTDEGRRFYE 78
Cdd:PRK04172   27 AEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAE 71
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-303 3.91e-03

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 37.67  E-value: 3.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 106 RVNVDSAFGHNVLAPRLGEFLARHPALSVELVV---RDRIGDLVAEGLDMAVRFGEAEPSGLISRQLARSRVLTCASPEY 182
Cdd:cd08426     3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVastADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243035561 183 -IARHgRPKHPSELAQGR----HECIRVRNPFTESyfewEFQRGEEIIPVnvqgrLVVNDSGSLIGAMLSGHGIGQPFEF 257
Cdd:cd08426    83 pLARQ-PSVTLAQLAGYPlalpPPSFSLRQILDAA----FARAGVQLEPV-----LISNSIETLKQLVAAGGGISLLTEL 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1243035561 258 SVRDLLESGRLVKL-----LPTWSDerypVYVYHRS-RELPAArVRAFIDFL 303
Cdd:cd08426   153 AVRREIRRGQLVAVpladpHMNHRQ----LELQTRAgRQLPAA-ASAFLQLL 199
 
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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