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Conserved domains on  [gi|1889702261|ref|WP_182738760|]
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LysR family transcriptional regulator [Pseudoalteromonas sp. SG45-1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-299 1.42e-58

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.42e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDqLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:COG0583     1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSL--SDEL-STLGRDDVDIAIRGGYAPNERVLAIK 157
Cdd:COG0583    80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLvDALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 158 LMDNGFIPVASPCYlqkygvptnvmELKGHSglyfktpagptpwlckvdeqwhdvsgpavAISNNGSwLAKKAC-NGEGI 236
Cdd:COG0583   160 LGEERLVLVASPDH-----------PLARRA-----------------------------PLVNSLE-ALLAAVaAGLGI 198

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1889702261 237 LMSTRWALDSYLESGQLQELKFEHELaisqnATMAVYLLYQKQRYLVPKVKAAVDFLVQRIKS 299
Cdd:COG0583   199 ALLPRFLAADELAAGRLVALPLPDPP-----PPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-299 1.42e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.42e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDqLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:COG0583     1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSL--SDEL-STLGRDDVDIAIRGGYAPNERVLAIK 157
Cdd:COG0583    80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLvDALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 158 LMDNGFIPVASPCYlqkygvptnvmELKGHSglyfktpagptpwlckvdeqwhdvsgpavAISNNGSwLAKKAC-NGEGI 236
Cdd:COG0583   160 LGEERLVLVASPDH-----------PLARRA-----------------------------PLVNSLE-ALLAAVaAGLGI 198

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1889702261 237 LMSTRWALDSYLESGQLQELKFEHELaisqnATMAVYLLYQKQRYLVPKVKAAVDFLVQRIKS 299
Cdd:COG0583   199 ALLPRFLAADELAAGRLVALPLPDPP-----PPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-293 6.87e-51

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: 166.46  E-value: 6.87e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLESG 251
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1889702261 252 QLQELkfeheLAISQNATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08422   161 RLVRV-----LPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
5-293 8.55e-38

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 135.93  E-value: 8.55e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   5 KAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVR 84
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  85 SYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFI 164
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRI 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 165 PVASPCYLQKYGVPTNVMELKGHSGLYFKT-PAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWA 243
Cdd:PRK09801  169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKErDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1889702261 244 LDSYLESGQLQELKFEHelaiSQNATmaVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:PRK09801  249 VLPFLESGKLVQVLPEY----AQSAN--IWAVYREPLYRSMKLRVCVEFL 292
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 2.75e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.13  E-value: 2.75e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQ 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-296 2.22e-20

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: 88.83  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MD--QLKAiryFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQ 78
Cdd:NF040786    1 MNlkQLEA---FVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  79 SHETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDE---LSTLGRDDVDIAIRGGYAPNERVLA 155
Cdd:NF040786   78 LEEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSikvIELLLEGEVDIGFTGTKLEKKRLVY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 156 IKLMDNGFIpVASPCYLQKYGVptnvmelkghsglyfKTPAGPTPWLCKVD-------------------------EQWH 210
Cdd:NF040786  158 TPFYKDRLV-LITPNGTEKYRM---------------LKEEISISELQKEPfimreegsgtrkeaekalkslgislEDLN 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 211 DVSgpavAISNNGSwlAKKAC-NGEGILMSTRWALDSYLESGQLQELKFeHELAISQNatmaVYLLYQKQRYLVPKVKAA 289
Cdd:NF040786  222 VVA----SLGSTEA--IKQSVeAGLGISVISELAAEKEVERGRVLIFPI-PGLPKNRD----FYLVYNKNRQLSPTAEAF 290


                  ....*..
gi 1889702261 290 VDFLVQR 296
Cdd:NF040786  291 LQFVKER 297
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-299 1.42e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 188.15  E-value: 1.42e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDqLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:COG0583     1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSL--SDEL-STLGRDDVDIAIRGGYAPNERVLAIK 157
Cdd:COG0583    80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLvDALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 158 LMDNGFIPVASPCYlqkygvptnvmELKGHSglyfktpagptpwlckvdeqwhdvsgpavAISNNGSwLAKKAC-NGEGI 236
Cdd:COG0583   160 LGEERLVLVASPDH-----------PLARRA-----------------------------PLVNSLE-ALLAAVaAGLGI 198

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1889702261 237 LMSTRWALDSYLESGQLQELKFEHELaisqnATMAVYLLYQKQRYLVPKVKAAVDFLVQRIKS 299
Cdd:COG0583   199 ALLPRFLAADELAAGRLVALPLPDPP-----PPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-293 6.87e-51

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: 166.46  E-value: 6.87e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLESG 251
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1889702261 252 QLQELkfeheLAISQNATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08422   161 RLVRV-----LPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
5-293 8.55e-38

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 135.93  E-value: 8.55e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   5 KAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVR 84
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  85 SYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFI 164
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRI 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 165 PVASPCYLQKYGVPTNVMELKGHSGLYFKT-PAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWA 243
Cdd:PRK09801  169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKErDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1889702261 244 LDSYLESGQLQELKFEHelaiSQNATmaVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:PRK09801  249 VLPFLESGKLVQVLPEY----AQSAN--IWAVYREPLYRSMKLRVCVEFL 292
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 18-299 1.08e-36

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 132.66  E-value: 1.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  18 SFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVRSYQTTpmGRLCIS 97
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAK--GALTVS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  98 SMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYA--PNERvlAIKLMDNGFIPVASPCYLQKY 175
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGnwPGLR--VEKLLDEYLLPVCSPALLNGG 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 176 GVPTNVMELKGHSGLYFKTPAGPTPWL--CKVDeqwhDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLESGQL 253
Cdd:PRK11139  178 KPLKTPEDLARHTLLHDDSREDWRAWFraAGLD----DLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRL 253

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1889702261 254 QELkFEHELaISQNatmAVYLLYQKQRYLVPKVKAAVDFLVQRIKS 299
Cdd:PRK11139  254 VCP-FDTVL-PSPN---AFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-295 2.04e-34

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 126.64  E-value: 2.04e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDQLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:PRK14997    1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNE------RVL 154
Cdd:PRK14997   81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFEdsdlvmRVL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 155 AiklmDNGFIPVASPCYLQKYGVPTNVMELKGHSGLYFKTPAGPTPW-LCKVDEQWHDVSGPAVAISNNGSWLAKKACNG 233
Cdd:PRK14997  161 A----DRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWeLYGPQGARAEVHFTPRMITTDMLALREAAMAG 236

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1889702261 234 EGILMSTRWALDSYLESGQLQELkfeheLAISQNATMAVYLLYQKQRYLVPKVKAAVDFLVQ 295
Cdd:PRK14997  237 VGLVQLPVLMVKEQLAAGELVAV-----LEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTE 293
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-296 1.08e-32

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: 119.54  E-value: 1.08e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAG--PTPWLCKVDEQWHDVSGP-AVAISNNGSWLAkKACNGEGILMSTRWALDSYL 248
Cdd:cd08472    81 LARHGTPRHPEDLERHRAVGYFSARTgrVLPWEFQRDGEEREVKLPsRVSVNDSEAYLA-AALAGLGIIQVPRFMVRPHL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1889702261 249 ESGQLQELkfeheLAISQNATMAVYLLYQKQRYLVPKVKAAVDFLVQR 296
Cdd:cd08472   160 ASGRLVEV-----LPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAEL 202
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 4.29e-32

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: 117.72  E-value: 4.29e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLESG 251
Cdd:cd08477    81 LARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1889702261 252 QLQELKFEHELAISQnatmaVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08477   161 RLVELLPDYLPPPRP-----MHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 1.69e-31

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: 116.16  E-value: 1.69e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGP-TPW-LCKVDEQWH-DVSGPAVaiSNNGSWLAKKACNGEGILMSTRWALDSYL 248
Cdd:cd08479    81 LERHGAPASPEDLARHDCLVIRENDEDfGLWrLRNGDGEATvRVRGALS--SNDGEVVLQWALDGHGIILRSEWDVAPYL 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1889702261 249 ESGQLQELKFEHELaisQNATmaVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08479   159 RSGRLVRVLPDWQL---PDAD--IWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 1.78e-29

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: 110.89  E-value: 1.78e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKVDEQWHD--VSGPAVAisNNGSWLAKKACNGEGILMSTRWALDSYLE 249
Cdd:cd08480    81 LARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDGGRIVAlpVSGNILV--NDGEALRRLALAGAGLARLALFHVADDIA 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1889702261 250 SGQLQELkFEHELAISQNATMAVYLlyqKQRYLVPKVKAAVDFL 293
Cdd:cd08480   159 AGRLVPV-LEEYNPGDREPIHAVYV---GGGRLPARVRAFLDFL 198
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-295 1.79e-29

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 113.70  E-value: 1.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDQLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:PRK10632    1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMD 160
Cdd:PRK10632   81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 161 NGFIPVASPCYLQKYGVPTNVMELKGHSGLYFK----------TPAGPTpwlCKVDEQWHDVSGPAVAISnngSWLAkka 230
Cdd:PRK10632  161 MPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSvrpdnefeliAPEGIS---TRLIPQGRFVTNDPQTLV---RWLT--- 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1889702261 231 cNGEGI----LMstrWALDSyLESGQLqELKFEHelaiSQNATMAVYLLYQKQRYLVPKVKAAVDFLVQ 295
Cdd:PRK10632  232 -AGAGIayvpLM---WVIDE-INRGEL-EILFPR----YQSDPRPVYALYTEKDKLPLKVQVCINYLTD 290
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 1.94e-28

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: 108.03  E-value: 1.94e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIR-GGYAPNERVLAIKLMDNGFIPVASPC 170
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRiGELADSTGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 171 YLQKYGVPTNVMELKGHSGLYFKTPAGPTPW-LCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLE 249
Cdd:cd08475    81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWrLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1889702261 250 SGQLQELKFEHELaisqnATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08475   161 RGELVEVLPELAP-----EGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-295 1.08e-26

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: 103.54  E-value: 1.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLyfktPAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLESG 251
Cdd:cd08470    81 LERHGTPHSLADLDRHNCL----LGTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAG 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1889702261 252 QLQELkfeheLAISQNATMAVYLLYQKQRYLVPKVKAAVDFLVQ 295
Cdd:cd08470   157 RLVPV-----LEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-296 8.65e-25

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: 98.37  E-value: 8.65e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKVDEQWHDVS-GPAVAISNNGSWLAkKACNGEGIlmsTRwaLDSY--- 247
Cdd:cd08471    81 LARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRvRPRLTVNTVEAAIA-AALAGLGL---TR--VLSYqva 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1889702261 248 --LESGQLQEL--KFEHELaisqnatMAVYLLYQKQRYLVPKVKAAVDFLVQR 296
Cdd:cd08471   155 eeLAAGRLQRVleDFEPPP-------LPVHLVHPEGRLAPAKVRAFVDFAVPR 200
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-143 9.70e-25

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 100.80  E-value: 9.70e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETV 83
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1889702261  84 RSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVslsDELS------TLGRDDVDIAI 143
Cdd:PRK11242   83 HDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTI---REMSqerieaLLADDELDVGI 145
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
18-299 3.05e-23

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 96.99  E-value: 3.05e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  18 SFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVRSYQTTpmGRLCIS 97
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELS--GTLTVY 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  98 SMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCYLQKYGV 177
Cdd:PRK10086  108 SRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAERHAL 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 178 PTNVMELKG----HSGLYFKTPAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLA-KKACNGEGILMSTRWALDSYLESGQ 252
Cdd:PRK10086  188 TGNPDNLRHctllHDRQAWSNDSGTDEWHSWAQHFGVNLLPPSSGIGFDRSDLAvIAAMNHIGVAMGRKRLVQKRLASGE 267

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1889702261 253 L------QELKFEHelaisqnatmAVYLLYQKQRyLVPKVKAAVDFLVQRIKS 299
Cdd:PRK10086  268 LvapfgdMEVKCHQ----------HYYVTTLPGR-QWPKIEAFIDWLKEQVKT 309
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 3.92e-23

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: 94.23  E-value: 3.92e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISsmVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08476     1 GRLRVS--LPLVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 172 LQKYGVPTNVMELKGHSGLYFKTPAGPT--PWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRWALDSYLE 249
Cdd:cd08476    79 LARHGTPETPADLAEHACLRYRFPTTGKlePWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALA 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1889702261 250 SGQLQELKFEHELAISQnatmaVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08476   159 DGRLVTVLDDYVEERGQ-----FRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-293 1.54e-22

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: 92.52  E-value: 1.54e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  90 PMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIR-GGYAPNERVlAIKLMDNG-FIPVA 167
Cdd:cd08474     1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRlGESVEKDMV-AVPLGPPLrMAVVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 168 SPCYLQKYGVPTNVMELKGHS--GLYFKTPAGPTPW-LCKVDEQWH-DVSGPAVAisNNGSWLAKKACNGEGILMSTRWA 243
Cdd:cd08474    80 SPAYLARHGTPEHPRDLLNHRciRYRFPTSGALYRWeFERGGRELEvDVEGPLIL--NDSDLMLDAALDGLGIAYLFEDL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1889702261 244 LDSYLESGQLQELkfeheLAISQNATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08474   158 VAEHLASGRLVRV-----LEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-293 3.81e-22

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: 91.49  E-value: 3.81e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  93 RLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCYL 172
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 173 QKYGvPTNVMELKG----HSGlyfKTPAGPTPWLCKVdeQWHDVSGPAVAISNNGSWLAKKACNGEGILMsTRWAL-DSY 247
Cdd:cd08432    81 AGLP-LLSPADLARhtllHDA---TRPEAWQWWLWAA--GVADVDARRGPRFDDSSLALQAAVAGLGVAL-APRALvADD 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1889702261 248 LESGQLQELkFEHELAisqnATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08432   154 LAAGRLVRP-FDLPLP----SGGAYYLVYPPGRAESPAVAAFRDWL 194
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-293 1.73e-21

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: 89.71  E-value: 1.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  90 PMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASP 169
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 170 CYLQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKV-DEQWHDVSgPAVAiSNNGSWLAKKACNGEGILMSTRWALDSYL 248
Cdd:cd08478    81 DYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDaDGNLLKIQ-PTIT-ASSGETLRQLALSGCGIACLSDFMTDKDI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1889702261 249 ESGQLQELkFEHElaiSQNATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08478   159 AEGRLIPL-FAEQ---TSDVRQPINAVYYRNTALSLRIRCFIDFL 199
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 2.75e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.13  E-value: 2.75e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQ 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-296 4.06e-21

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 88.89  E-value: 4.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  92 GRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDE---LSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVAS 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSeelLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 169 PCYLQKYGVPTNVMELKGHSGLYFKTPAGPTPWLckvdEQWHDVSG--PAVAISNNgSWLAKKAC--NGEGILMSTRWAL 244
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLL----DRALRAAGlrPRVVLEVN-SLEALLQLvaAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1889702261 245 DSYLESGQLQELKFEHElaisqNATMAVYLLYQKQRYLVPKVKAAVDFLVQR 296
Cdd:pfam03466 157 ARELADGRLVALPLPEP-----PLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-296 2.22e-20

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: 88.83  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MD--QLKAiryFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQ 78
Cdd:NF040786    1 MNlkQLEA---FVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  79 SHETVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDE---LSTLGRDDVDIAIRGGYAPNERVLA 155
Cdd:NF040786   78 LEEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSikvIELLLEGEVDIGFTGTKLEKKRLVY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 156 IKLMDNGFIpVASPCYLQKYGVptnvmelkghsglyfKTPAGPTPWLCKVD-------------------------EQWH 210
Cdd:NF040786  158 TPFYKDRLV-LITPNGTEKYRM---------------LKEEISISELQKEPfimreegsgtrkeaekalkslgislEDLN 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 211 DVSgpavAISNNGSwlAKKAC-NGEGILMSTRWALDSYLESGQLQELKFeHELAISQNatmaVYLLYQKQRYLVPKVKAA 289
Cdd:NF040786  222 VVA----SLGSTEA--IKQSVeAGLGISVISELAAEKEVERGRVLIFPI-PGLPKNRD----FYLVYNKNRQLSPTAEAF 290


                  ....*..
gi 1889702261 290 VDFLVQR 296
Cdd:NF040786  291 LQFVKER 297
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 4-159 5.57e-17

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 79.34  E-value: 5.57e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETV 83
Cdd:PRK11233    3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  84 -RSYQTtpmgrlcISSMVSFG-------DKMLLPLLDEFSALYPEIIL------DVSLSDELSTlGRddVDIAIRGGYAP 149
Cdd:PRK11233   83 hNVGQA-------LSGQVSIGlapgtaaSSLTMPLLQAVRAEFPGIVLylhensGATLNEKLMN-GQ--LDMAVIYEHSP 152

                         170
                  ....*....|
gi 1889702261 150 NERVLAIKLM 159
Cdd:PRK11233  153 VAGLSSQPLL 162
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 3-142 1.84e-13

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 69.41  E-value: 1.84e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   3 QLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQ---- 78
Cdd:PRK09906    2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKaklr 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1889702261  79 SHETVRSYQTTPMGRLCISSMvsfgdKMLLPLLDEFSALYPEIILD-VSL--SDELSTLGRDDVDIA 142
Cdd:PRK09906   82 ARKIVQEDRQLTIGFVPSAEV-----NLLPKVLPMFRLRHPDTLIElVSLitTQQEEKLRRGELDVG 143
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 94-293 1.30e-12

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: 65.39  E-value: 1.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  94 LCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASPCYLQ 173
Cdd:cd08481     2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 174 KYGVptNVMELKGHSGLYFKTpAGPTPWlckvdEQW---HDVSGPAvAISNNG----SWLAKKACNGEGILMSTRWALDS 246
Cdd:cd08481    82 GRAL--AAPADLAHLPLLQQT-TRPEAW-----RDWfeeVGLEVPT-AYRGMRfeqfSMLAQAAVAGLGVALLPRFLIEE 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1889702261 247 YLESGQLQELkFEHELAisqnATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08481   153 ELARGRLVVP-FNLPLT----SDKAYYLVYPEDKAESPPVQAFRDWL 194
PRK09986 PRK09986
LysR family transcriptional regulator;
4-143 2.62e-12

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 65.90  E-value: 2.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETV 83
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1889702261  84 RSYQTTPMGRLCIsSMVsfGDKM---LLPLLDEFSALYPEIilDVSLSD-----ELSTLGRDDVDIAI 143
Cdd:PRK09986   89 EQIGRGEAGRIEI-GIV--GTALwgrLRPAMRHFLKENPNV--EWLLRElspsmQMAALERRELDAGI 151
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-151 4.54e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.43  E-value: 4.54e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDQLKAIRyfiKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:CHL00180    7 LDQLRILK---AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETC 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSFGdKMLLP-LLDEFSALYPEII--LDVSLSDELS-TLGRDDVDIAIRGGYAPNE 151
Cdd:CHL00180   84 RALEDLKNLQRGTLIIGASQTTG-TYLMPrLIGLFRQRYPQINvqLQVHSTRRIAwNVANGQIDIAIVGGEVPTE 157
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-77 3.58e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.52  E-value: 3.58e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1889702261   1 MDQlKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLE 77
Cdd:PRK10094    2 FDP-ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-175 3.87e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 62.30  E-value: 3.87e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDQLKAiryFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRsTRIVKLTEVGQIYYNDVQQIlNQLEqsH 80
Cdd:PRK13348    4 YKQLEA---LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-ALLE--A 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  81 ETVRSYQTTPMGRLCISSMVSfGDKM---LLPLLDEFSAlYPEIILDVSLSDE---LSTLGRDDV-------DIAIRGGY 147
Cdd:PRK13348   77 DLLSTLPAERGSPPTLAIAVN-ADSLatwFLPALAAVLA-GERILLELIVDDQdhtFALLERGEVvgcvstqPKPMRGCL 154

                         170       180
                  ....*....|....*....|....*...
gi 1889702261 148 APNervlaIKLMDngFIPVASPCYLQKY 175
Cdd:PRK13348  155 AEP-----LGTMR--YRCVASPAFAARY 175
PRK09791 PRK09791
LysR family transcriptional regulator;
3-125 2.44e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.08  E-value: 2.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   3 QLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHET 82
Cdd:PRK09791    6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1889702261  83 VRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDV 125
Cdd:PRK09791   86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-143 1.07e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 54.82  E-value: 1.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  28 VPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVRSYQTTPMGRLCISSMV----SFg 103
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVtaaySH- 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1889702261 104 dkmLLPLLDEFSALYPEIilDVSLS-----DELSTLGRDDVDIAI 143
Cdd:PRK11716   82 ---LPPILDRFRAEHPLV--EIKLTtgdaaDAVEKVQSGEADLAI 121
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-78 1.93e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.39  E-value: 1.93e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1889702261   5 KAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRsTRIVKLTEVGQIYYNDVQQiLNQLEQ 78
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQ-VRLLEA 76
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-149 2.81e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 54.25  E-value: 2.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   1 MDQLKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSH 80
Cdd:PRK15421    1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1889702261  81 ETVRSYQTTpmgRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLS---DELSTLGRDDVDIAIRGGYAP 149
Cdd:PRK15421   81 QACNEPQQT---RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGvtfDPQPALQQGELDLVMTSDILP 149
PRK10341 PRK10341
transcriptional regulator TdcA;
10-185 3.15e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.10  E-value: 3.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  10 FIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVRS--YQ 87
Cdd:PRK10341   15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGmsSE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  88 TTPMGRLCISSMVSFgdKMLLPLLDEFSALYPEI---ILDVSLSDELSTLGRDDVDIAIrgGYAPNERVL----AIKLMD 160
Cdd:PRK10341   95 AVVDVSFGFPSLIGF--TFMSDMINKFKEVFPKAqvsMYEAQLSSFLPAIRDGRLDFAI--GTLSNEMKLqdlhVEPLFE 170

                         170       180
                  ....*....|....*....|....*
gi 1889702261 161 NGFIPVASPcyLQKYGVPTNVMELK 185
Cdd:PRK10341  171 SEFVLVASK--SRTCTGTTTLESLK 193
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-293 3.15e-08

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: 52.94  E-value: 3.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  90 PMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNE------RVLAiklmDNGF 163
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEdsslvmRVLG----QSRQ 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 164 IPVASPCYLQKYGVPTNVMELKGHSGLYFKTPAGPTPWlckvdeQWHDVSGPAVAI-------SNNGSWLAKKACNGEGI 236
Cdd:cd08473    77 RLVASPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSW------RLEGPDGESITVrhrprlvTDDLLTLRQAALAGVGI 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1889702261 237 LMSTRWALDSYLESGQLQELKFEHELAISQnatmaVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd08473   151 ALLPDHLCREALRAGRLVRVLPDWTPPRGI-----VHAVFPSRRGLLPAVRALIDFL 202
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-143 2.83e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 51.10  E-value: 2.83e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  13 VVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEqshETVRSYQTTPMG 92
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQ---ETRRQCQQVANG 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1889702261  93 -----RLCISSMVSfGDKMlLPLLDEFSALYPEIILDVSLS------DELSTlGRddVDIAI 143
Cdd:PRK11074   90 wrgqlSIAVDNIVR-PDRT-RQLIVDFYRHFDDVELIIRQEvfngvwDALAD-GR--VDIAI 146
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
10-264 3.67e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 50.82  E-value: 3.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  10 FIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHETVRSYQTT 89
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  90 PMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTL--GRDDVDIAIRggyapNERVLA-----IKLMDNG 162
Cdd:PRK10082   99 AQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLreGQSDCIFSFH-----DEDLLEapfdhIRLFESQ 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 163 FIPVaspCYLQKYGVPTNVMELKGHSGLYFKTPAGPTPWLCKVDEQWHDVSGPAVAISNNGSWLAKKACNGEGILMSTRW 242
Cdd:PRK10082  174 LFPV---CASDEHGEALFNLAQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGCGIAWLPEY 250

                         250       260
                  ....*....|....*....|..
gi 1889702261 243 ALDSYLESGQLQELKFEhELAI 264
Cdd:PRK10082  251 AIQQEIRSGQLVVLNRD-ELVI 271
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-293 5.56e-07

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 49.14  E-value: 5.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  93 RLCISSMVSFGDKMLLPLLDEFSALYP--EIILDVSLSDELST-LGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASP 169
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPgvELSLVEGGSSELLEaLLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 170 CYLQKYGVPTNVMELKGHSglYFKTPAGPTPWLcKVDE--QWHDVSgPAVAISNNgSWLAKKAC--NGEGILMSTRWALD 245
Cdd:cd05466    81 DHPLAKRKSVTLADLADEP--LILFERGSGLRR-LLDRafAEAGFT-PNIALEVD-SLEAIKALvaAGLGIALLPESAVE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1889702261 246 sYLESGQLQELKFEHElaisqNATMAVYLLYQKQRYLVPKVKAAVDFL 293
Cdd:cd05466   156 -ELADGGLVVLPLEDP-----PLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 94-293 7.66e-07

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: 48.50  E-value: 7.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261  94 LCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIR---GGYAPNErvlAIKLMDNGFIPVASPC 170
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRygnGDWPGLE---SEPLTAAPFVVVAAPG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261 171 YLQKygvpTNVMELKGHSGLyfktpagptPWLCKVD--EQW-----HDV---SGPAVAISNNGSWL-AKKAcnGEGILMS 239
Cdd:cd08483    79 LLGD----RKVDSLADLAGL---------PWLQERGtnEQRvwlasMGVvpdLERGVTFLPGQLVLeAARA--GLGLSIQ 143

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1889702261 240 TRWALDSYLESGQLQELkFEHElaisqNATMAVYLLyQKQRYLVPKVKAAVDFL 293
Cdd:cd08483   144 ARALVEPDIAAGRLTVL-FEEE-----EEGLGYHIV-TRPGVLRPAAKAFVRWL 190
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-129 1.88e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 45.45  E-value: 1.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYndvQQILNQLEQSHETV 83
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY---PRALALLEQAVEIE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1889702261  84 RSYQTTpMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSD 129
Cdd:PRK10837   82 QLFRED-NGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGN 126
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
5-128 2.02e-05

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 45.43  E-value: 2.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   5 KAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQ---ILNQLEQshe 81
Cdd:PRK15243    7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKShyiFLHALEQ--- 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1889702261  82 tvrsyQTTPMGRlcissmvsfgDKMLLPLLDEfsaLYPEIILDVSLS 128
Cdd:PRK15243   84 -----EIGPTGK----------TKQLEIIFDE---IYPESLKNLIIS 112
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-66 3.83e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 44.61  E-value: 3.83e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1889702261   9 YFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYY 66
Cdd:PRK11062   11 YFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF 68
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-125 1.90e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVGQIYYNDVQQI---LNQLEQSH 80
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAA 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1889702261  81 ETVRSYQTtpmGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDV 125
Cdd:PRK11013   86 ESLREFRQ---GQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNI 127
cbl PRK12679
HTH-type transcriptional regulator Cbl;
3-143 2.22e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.10  E-value: 2.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   3 QLKAIRYFIKvvETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATL-LKRSTRIVKLTEVGQIYYNDVQQILNQLEQSHE 81
Cdd:PRK12679    5 QLKIIREAAR--QDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1889702261  82 TVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILDV---SLSDELSTLGRDDVDIAI 143
Cdd:PRK12679   83 LADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELiqgTPQEIATLLQNGEADIGI 147
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 7-62 1.04e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 40.01  E-value: 1.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1889702261   7 IR---YFIKVVETGSFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKRSTRIVKLTEVG 62
Cdd:PRK11151    3 IRdleYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 107-171 2.81e-03

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


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 38.15  E-value: 2.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1889702261 107 LLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAP-NERVLAIKLMDNGFIPVASPCY 171
Cdd:cd08482    15 LIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFPERVGPVCSPSL 80
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 94-169 4.52e-03

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: 37.52  E-value: 4.52e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1889702261  94 LCISSMVSFGDKMLLPLLDEFSALYPEIILDVSLSDELSTLGRDDVDIAIRGGYAPNERVLAIKLMDNGFIPVASP 169
Cdd:cd08487     2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSP 77
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
4-143 5.28e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 38.03  E-value: 5.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889702261   4 LKAIRYFIKVVETG-SFTKAAKAFDVPPSSLSRRVADLEKSLGATLLKR-STRIVKLTEVGQIYYNDVQQILNQLEQSHE 81
Cdd:PRK12684    3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERILQEVENLKR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1889702261  82 TVRSYQTTPMGRLCISSMVSFGDKMLLPLLDEFSALYPEIILD------VSLSDELSTlgrDDVDIAI 143
Cdd:PRK12684   83 VGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSilqgspTQIAEMVLH---GQADLAI 147
 
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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