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Conserved domains on  [gi|16130715|ref|NP_417288|]
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DNA-binding transcriptional dual regulator GcvA [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

transcriptional regulator GcvA( domain architecture ID 11485222)

transcriptional regulator GcvA is a LysR-type transcriptional regulator protein that mediates activation of gcv by glycine and repression by purines

Gene Ontology:  GO:0006355|GO:0006351|GO:0003677
PubMed:  8188587|19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-297 0e+00

DNA-binding transcriptional activator GcvA; Provisional


:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 583.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    1 MSKRLPPLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   81 TEATRKLQARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKL 160
Cdd:PRK11139  81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  161 YAEYLLPVCSPLLLTGEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALAN 240
Cdd:PRK11139 161 LDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 16130715  241 NVMAQSEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWILAKAAAEQE 297
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-297 0e+00

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 583.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    1 MSKRLPPLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   81 TEATRKLQARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKL 160
Cdd:PRK11139  81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  161 YAEYLLPVCSPLLLTGEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALAN 240
Cdd:PRK11139 161 LDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 16130715  241 NVMAQSEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWILAKAAAEQE 297
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-288 7.57e-85

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: 253.27  E-value: 7.57e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  95 ALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLLL 174
Cdd:cd08432   1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 175 TGEKPLkTPEDLAKHTLLHDASR-RDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRL 253
Cdd:cd08432  81 AGLPLL-SPADLARHTLLHDATRpEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                       170       180       190
                ....*....|....*....|....*....|....*
gi 16130715 254 VCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08432 160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-294 6.44e-62

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 197.01  E-value: 6.44e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   7 PLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRK 86
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  87 LQARSA--KGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAV--DRQEDKLAD-DVDVAIFYGRGNWPGLRVEKLY 161
Cdd:COG0583  82 LRALRGgpRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDALLEgELDLAIRLGPPPDPGLVARPLG 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 162 AEYLLPVCSPllltgekplktpedlakhtllhdasrrdwqtytrqlglNHINVQQGPIFSHSAMVLQAAIHGQGVALANN 241
Cdd:COG0583 162 EERLVLVASP--------------------------------------DHPLARRAPLVNSLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 16130715 242 VMAQSEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWILAKAAA 294
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-293 3.60e-31

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 115.85  E-value: 3.60e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAIFYGRGNWPGLRVEKLYAEYLLPVCS 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEEllDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   171 P-LLLTGEKPLkTPEDLAKHTLLH-DASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEI 248
Cdd:pfam03466  82 PdHPLARGEPV-SLEDLADEPLILlPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 16130715   249 EAGRLVC-PFNDVLVSkNAFYLVCHDSQAELGKIAAFRQWILAKAA 293
Cdd:pfam03466 161 ADGRLVAlPLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-297 0e+00

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 583.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    1 MSKRLPPLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   81 TEATRKLQARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKL 160
Cdd:PRK11139  81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  161 YAEYLLPVCSPLLLTGEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALAN 240
Cdd:PRK11139 161 LDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 16130715  241 NVMAQSEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWILAKAAAEQE 297
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-288 7.57e-85

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: 253.27  E-value: 7.57e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  95 ALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLLL 174
Cdd:cd08432   1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 175 TGEKPLkTPEDLAKHTLLHDASR-RDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRL 253
Cdd:cd08432  81 AGLPLL-SPADLARHTLLHDATRpEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                       170       180       190
                ....*....|....*....|....*....|....*
gi 16130715 254 VCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08432 160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-295 1.74e-66

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 210.24  E-value: 1.74e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    4 RLPPLNA-----LRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFS 78
Cdd:PRK10086   7 RNRLLNGwqlskLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   79 QLTEATRKLQARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRI----QAVDRQEDKladdVDVAIFYGRGNWPG 154
Cdd:PRK10086  87 TLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIltgnENVNFQRAG----IDLAIYFDDAPSAQ 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  155 LRVEKLYAEYLLPVCSPLLLTGEKPLKTPEDLAKHTLLHD------ASRRD-WQTYTRQLGLNHINVQQGPIFSHSAMVL 227
Cdd:PRK10086 163 LTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDrqawsnDSGTDeWHSWAQHFGVNLLPPSSGIGFDRSDLAV 242

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130715  228 QAAIHGQGVALANNVMAQSEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWiLAKAAAE 295
Cdd:PRK10086 243 IAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDW-LKEQVKT 309
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-294 6.44e-62

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 197.01  E-value: 6.44e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   7 PLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRK 86
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  87 LQARSA--KGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAV--DRQEDKLAD-DVDVAIFYGRGNWPGLRVEKLY 161
Cdd:COG0583  82 LRALRGgpRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDALLEgELDLAIRLGPPPDPGLVARPLG 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 162 AEYLLPVCSPllltgekplktpedlakhtllhdasrrdwqtytrqlglNHINVQQGPIFSHSAMVLQAAIHGQGVALANN 241
Cdd:COG0583 162 EERLVLVASP--------------------------------------DHPLARRAPLVNSLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 16130715 242 VMAQSEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWILAKAAA 294
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 96-288 6.00e-55

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: 176.72  E-value: 6.00e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLLLT 175
Cdd:cd08481   2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLA 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 176 GEkPLKTPEDLAKHTLLHDASRRD-WQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRLV 254
Cdd:cd08481  82 GR-ALAAPADLAHLPLLQQTTRPEaWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLV 160

                       170       180       190
                ....*....|....*....|....*....|....
gi 16130715 255 CPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08481 161 VPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 96-288 1.86e-40

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 139.43  E-value: 1.86e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLLlt 175
Cdd:cd08484   2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPEL-- 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 176 gEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNHINVqQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRLVC 255
Cdd:cd08484  80 -ARRLSEPADLANETLLRSYRADEWPQWFEAAGVPPPPI-NGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQ 157

                       170       180       190
                ....*....|....*....|....*....|...
gi 16130715 256 PFnDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08484 158 PF-KITVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 96-288 4.71e-38

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: 133.05  E-value: 4.71e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPlllT 175
Cdd:cd08487   2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSP---E 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 176 GEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNHINVqQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRLVC 255
Cdd:cd08487  79 IAKRLSHPADLINETLLRSYRTDEWLQWFEAANMPPIKI-RGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQ 157

                       170       180       190
                ....*....|....*....|....*....|...
gi 16130715 256 PFnDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08487 158 PF-KIEVETGSYWLTWLKSKPMTPAMELFRQWI 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 96-288 6.56e-36

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


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 127.65  E-value: 6.56e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLLlt 175
Cdd:cd08488   2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPEL-- 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 176 gEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNH-INVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRLV 254
Cdd:cd08488  80 -ARQLREPADLARHTLLRSYRADEWPQWFEAAGVGHpCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALV 158

                       170       180       190
                ....*....|....*....|....*....|....
gi 16130715 255 CPFnDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08488 159 QPF-ATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 95-288 3.52e-33

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: 120.53  E-value: 3.52e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  95 ALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLLL 174
Cdd:cd08483   1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 175 tGEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLNHINVqQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRLV 254
Cdd:cd08483  81 -GDRKVDSLADLAGLPWLQERGTNEQRVWLASMGVVPDLE-RGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRLT 158

                       170       180       190
                ....*....|....*....|....*....|....
gi 16130715 255 CPFNDVLVSKnAFYLVCHDSQAElGKIAAFRQWI 288
Cdd:cd08483 159 VLFEEEEEGL-GYHIVTRPGVLR-PAAKAFVRWL 190
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-293 3.60e-31

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 115.85  E-value: 3.60e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAIFYGRGNWPGLRVEKLYAEYLLPVCS 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEEllDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   171 P-LLLTGEKPLkTPEDLAKHTLLH-DASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEI 248
Cdd:pfam03466  82 PdHPLARGEPV-SLEDLADEPLILlPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 16130715   249 EAGRLVC-PFNDVLVSkNAFYLVCHDSQAELGKIAAFRQWILAKAA 293
Cdd:pfam03466 161 ADGRLVAlPLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 95-288 7.03e-30

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: 112.11  E-value: 7.03e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  95 ALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWP-GLRVEKLYAEYLLPVCSPlL 173
Cdd:cd08482   1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPaGMQVIELFPERVGPVCSP-S 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKT--PEDLAKHTLLHDASRRD-WQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEA 250
Cdd:cd08482  80 LAPTVPLRQapAAALLGAPLLHTRSRPQaWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLAS 159

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 16130715 251 GRLVCPFNdvLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08482 160 GRLVAPWG--FIETGSHYVLLRPARLRDSRAGALADWL 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-231 2.29e-26

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 105.42  E-value: 2.29e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL 87
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   88 Q--ARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAV--DRQEDKLADD-VDVAIFYGRGNWPGLRVEKLYA 162
Cdd:PRK11242  83 HdvADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMsqERIEALLADDeLDVGIAFAPVHSPEIEAQPLFT 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  163 EYL-LPVCSPLLLTGEKPLKTPEDLAKH--TLLHD--ASRRDWQTYTRQLGL--------NHIN-----VQQGPIfshsA 224
Cdd:PRK11242 163 ETLaLVVGRHHPLAARRKALTLDELADEplVLLSAefATREQIDRYFRRHGVtprvaieaNSISavleiVRRGRL----A 238


                 ....*..
gi 16130715  225 MVLQAAI 231
Cdd:PRK11242 239 TLLPAAI 245
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-288 1.75e-24

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: 97.90  E-value: 1.75e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLL 173
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKTPEDLAKHTLL---HDASRRDWQtYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEA 250
Cdd:cd08422  81 LARHGTPQTPEDLARHRCLgyrLPGRPLRWR-FRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 16130715 251 GRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd08422 160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 5.07e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 92.45  E-value: 5.07e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715     8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQ 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-172 1.16e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 75.58  E-value: 1.16e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEAtrKL 87
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKA--KL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   88 QAR---SAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAV--DRQEDKLAD-DVDVAIFYGRGNWPGLRVEKLY 161
Cdd:PRK09906  81 RARkivQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLitTQQEEKLRRgELDVGFMRHPVYSDEIDYLELL 160

                        170
                 ....*....|....
gi 16130715  162 AE---YLLPVCSPL 172
Cdd:PRK09906 161 DEplvVVLPVDHPL 174
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-128 1.13e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 73.13  E-value: 1.13e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQsYFLDIKE-IFSQLTEATRK 86
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGE-LLLRYGNrILALCEETCRA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 16130715   87 LQARSA--KGALTVSllPSFAI-HWLVPRLSS-FNSAYPGIDVRIQ 128
Cdd:CHL00180  86 LEDLKNlqRGTLIIG--ASQTTgTYLMPRLIGlFRQRYPQINVQLQ 129
PRK09986 PRK09986
LysR family transcriptional regulator;
8-125 1.20e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 72.83  E-value: 1.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL 87
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 16130715   88 Q--ARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDV 125
Cdd:PRK09986  89 EqiGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW 128
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 94-284 2.06e-14

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: 70.45  E-value: 2.06e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLL 173
Cdd:cd08478   3 GLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDY 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKTPEDLAKHTLL---HDASRRDWQTYTRQLGLNHInvQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEA 250
Cdd:cd08478  83 LARHGTPQSIEDLAQHQLLgftEPASLNTWPIKDADGNLLKI--QPTITASSGETLRQLALSGCGIACLSDFMTDKDIAE 160

                       170       180       190
                ....*....|....*....|....*....|....*
gi 16130715 251 GRLVCPFNDVLVS-KNAFYLVCHDSQAELGKIAAF 284
Cdd:cd08478 161 GRLIPLFAEQTSDvRQPINAVYYRNTALSLRIRCF 195
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 4.25e-14

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: 69.57  E-value: 4.25e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLyAEYLLPVC-SPL 172
Cdd:cd08477   1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPL-APYRMVLCaSPD 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 173 LLTGEKPLKTPEDLAKHTLL---HDASRRDWQtYTRQLGlnHINVQQGPIFS--HSAMVLQAAIHGQGVALANNVMAQSE 247
Cdd:cd08477  80 YLARHGTPTTPEDLARHECLgfsYWRARNRWR-LEGPGG--EVKVPVSGRLTvnSGQALRVAALAGLGIVLQPEALLAED 156


                ....*..
gi 16130715 248 IEAGRLV 254
Cdd:cd08477 157 LASGRLV 163
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-288 1.37e-13

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 68.01  E-value: 1.37e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPL 172
Cdd:cd05466   2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSEllEALLEgELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 173 -LLTGEKPLkTPEDLAKHTL-LHDASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQsEIEA 250
Cdd:cd05466  82 hPLAKRKSV-TLADLADEPLiLFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELAD 159

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 16130715 251 GRLV-CPFNDVLVSkNAFYLVCHDSQAELGKIAAFRQWI 288
Cdd:cd05466 160 GGLVvLPLEDPPLS-RTIGLVWRKGRYLSPAARAFLELL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
22-254 1.50e-13

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 69.68  E-value: 1.50e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   22 SFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYF---LDIKEIFSQLTEATRKLQARsAKGALTV 98
Cdd:PRK09801  22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYehaLEILTQYQRLVDDVTQIKTR-PEGMIRI 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   99 SLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIfygRGN--WPGLRVEKLYAEYLLPVC-SPLLLT 175
Cdd:PRK09801 101 GCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDI---RINdeIPDYYIAHLLTKNKRILCaAPEYLQ 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  176 GEKPLKTPEDLAKHTLLHdASRRDWQTYTRQLGlnhiNVQQ-------GPIFSHSA-MVLQAAIHGQGVALANNVMAQSE 247
Cdd:PRK09801 178 KYPQPQSLQELSRHDCLV-TKERDMTHGIWELG----NGQEkksvkvsGHLSSNSGeIVLQWALEGKGIMLRSEWDVLPF 252


                 ....*..
gi 16130715  248 IEAGRLV 254
Cdd:PRK09801 253 LESGKLV 259
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 2.03e-13

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: 67.54  E-value: 2.03e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLyAEYLLPVC-SPL 172
Cdd:cd08472   1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRL-GELRMVTCaSPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 173 LLTGEKPLKTPEDLAKHTLLHDASRR-----DWQtYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSE 247
Cdd:cd08472  80 YLARHGTPRHPEDLERHRAVGYFSARtgrvlPWE-FQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPH 158


                ....*..
gi 16130715 248 IEAGRLV 254
Cdd:cd08472 159 LASGRLV 165
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-210 4.12e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 68.51  E-value: 4.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    3 KRLPPLNALRvfdaaaRHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTE 82
Cdd:PRK15421   5 KHLKTLQALR------NCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   83 AtrkLQA--RSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQA---VDRQEDKLADDVDVAIFYGRGNWPGLRV 157
Cdd:PRK15421  79 A---LQAcnEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSgvtFDPQPALQQGELDLVMTSDILPRSGLHY 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 16130715  158 EKLYAEYLLPVCSPLLLTGEKPLKTPEDLAKHTLL---HDASRRD-WQTYTRQLGLN 210
Cdd:PRK15421 156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLiypVQRSRLDvWRHFLQPAGVS 212
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-94 5.31e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 68.04  E-value: 5.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   10 ALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLtEATRKLQA 89
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKM-QETRRQCQ 84


                 ....*
gi 16130715   90 RSAKG 94
Cdd:PRK11074  85 QVANG 89
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 8.88e-13

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: 66.04  E-value: 8.88e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIfygRGNWP-----GLRVEKLYAEYLLPV 168
Cdd:cd08473   3 GTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVAL---RVRFPpledsSLVMRVLGQSRQRLV 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 169 CSPLLLTGEKPLKTPEDLAKHTLLH--DASRRD-WQTYTRQLGLNHINVQqgPIFSHSAMVL--QAAIHGQGVALANNVM 243
Cdd:cd08473  80 ASPALLARLGRPRSPEDLAGLPTLSlgDVDGRHsWRLEGPDGESITVRHR--PRLVTDDLLTlrQAALAGVGIALLPDHL 157

                       170
                ....*....|.
gi 16130715 244 AQSEIEAGRLV 254
Cdd:cd08473 158 CREALRAGRLV 168
PRK09791 PRK09791
LysR family transcriptional regulator;
8-127 1.03e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.09  E-value: 1.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL 87
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 16130715   88 QAR--SAKGALTVSLLPSFAiHWLVPR-LSSFNSAYPGIDVRI 127
Cdd:PRK09791  87 RQRqgQLAGQINIGMGASIA-RSLMPAvISRFHQQHPQVKVRI 128
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-145 3.42e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 65.82  E-value: 3.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL 87
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130715   88 QARSAKGALTV--------SLLPSFaihwlvprLSSFNSAYP--GIDVRIQAVDRQEDKLADD-VDVAI 145
Cdd:PRK15092  93 MYSNLQGVLTIgasddtadTILPFL--------LNRVSSVYPklALDVRVKRNAFMMEMLESQeVDLAV 153
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
22-262 7.94e-12

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 64.69  E-value: 7.94e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   22 SFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTE-----------ATRKLQAR 90
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESnlaelrggsdyAQRKIKIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   91 SAKgALTVSLLPSFAIHwlVPRLssFNSAYPGIDVRiQAVDRQEDKLAD------DVDVAifygRGNWPGLRvekLYAEY 164
Cdd:PRK10082 107 AAH-SLSLGLLPSIISQ--MPPL--FTWAIEAIDVD-EAVDKLREGQSDcifsfhDEDLL----EAPFDHIR---LFESQ 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  165 LLPVCS-----PLLLTGEKPlktpedlakHTLLHDASRRDW------QTYTRqlglnHINVQQGPIF--SHSAMVLQAAI 231
Cdd:PRK10082 174 LFPVCAsdehgEALFNLAQP---------HFPLLNYSRNSYmgrlinRTLTR-----HSELSFSTFFvsSMSELLKQVAL 239

                        250       260       270
                 ....*....|....*....|....*....|.
gi 16130715  232 HGQGVALANNVMAQSEIEAGRLVCPFNDVLV 262
Cdd:PRK10082 240 DGCGIAWLPEYAIQQEIRSGQLVVLNRDELV 270
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-88 8.64e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 64.44  E-value: 8.64e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130715   10 ALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKLQ 88
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 1.23e-11

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: 62.74  E-value: 1.23e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLL 173
Cdd:cd08480   1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKTPEDLAKHTLLHDASRR---DW------QTYTRQLglnhinvqQGPIFSHSAMVL-QAAIHGQGVALANNVM 243
Cdd:cd08480  81 LARHGTPLTPQDLARHNCLGFNFRRalpDWpfrdggRIVALPV--------SGNILVNDGEALrRLALAGAGLARLALFH 152

                       170
                ....*....|.
gi 16130715 244 AQSEIEAGRLV 254
Cdd:cd08480 153 VADDIAAGRLV 163
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-145 2.41e-11

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 63.09  E-value: 2.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    5 LPPLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEAT 84
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16130715   85 RKLQARSAKGALTVSLL-PSFAIHWLV-PRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAI 145
Cdd:PRK14997  81 DAIAALQVEPRGIVKLTcPVTLLHVHIgPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAI 143
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 105-272 5.40e-11

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 60.97  E-value: 5.40e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 105 AIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSP-LLLTGEKPL 180
Cdd:cd08420  11 GEYLLPRLLARFRKRYPEVRVSLTIGNTEEiaERVLDgEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPdHPLAGRKEV 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 181 kTPEDLAKHTLL----HDASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIEAGRLVC- 255
Cdd:cd08420  91 -TAEELAAEPWIlrepGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVAl 169

                       170
                ....*....|....*..
gi 16130715 256 PFNDVLVSKNaFYLVCH 272
Cdd:cd08420 170 PVEGLRLTRP-FSLIYH 185
PRK12680 PRK12680
LysR family transcriptional regulator;
8-209 6.08e-11

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 62.33  E-value: 6.08e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAA-RHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSL-LLTEEGQSYFLDIKEIFSQL----T 81
Cdd:PRK12680   3 LTQLRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEAnnirT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   82 EATRklQARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAIFYGRGNWPG---- 154
Cdd:PRK12680  83 YAAN--QRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAalDLLGQgDADIAIVSTAGGEPSagia 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16130715  155 ---LRVEKLyaeYLLPVCSPLlltgEKPLKTPE--DLAKHTLL-HDASRRDWQTYTR---QLGL 209
Cdd:PRK12680 161 vplYRWRRL---VVVPRGHAL----DTPRRAPDmaALAEHPLIsYESSTRPGSSLQRafaQLGL 217
cbl PRK12679
HTH-type transcriptional regulator Cbl;
15-192 2.33e-10

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 60.59  E-value: 2.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   15 DAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLL-LTEEGQSyFLDIKEIFsqLTEAT--RKLQ--- 88
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKA-LLVIAERI--LNEASnvRRLAdlf 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   89 ARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDK---LADDVDVAIFYGR-GNWPGLRVEKLYAEY 164
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIAtllQNGEADIGIASERlSNDPQLVAFPWFRWH 167

                        170       180       190
                 ....*....|....*....|....*....|.
gi 16130715  165 ---LLPVCSPllLTGEKPLkTPEDLAKHTLL 192
Cdd:PRK12679 168 hslLVPHDHP--LTQITPL-TLESIAKWPLI 195
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-199 7.05e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 59.00  E-value: 7.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL 87
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   88 QA--RSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGrgnwpGLRVEKLYAEYL 165
Cdd:PRK10632  84 YAfnNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVG-----ALQDSSLFSRRL 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 16130715  166 --LP--VCSP--LLLTGEKPLKtPEDLAKHTLLHDASRRD 199
Cdd:PRK10632 159 gaMPmvVCAAksYLAQYGTPEK-PADLSSHSWLEYSVRPD 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-145 1.20e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 58.06  E-value: 1.20e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALR-VFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLL-LTEEGQSyFLDIKEIFSQLTEATR 85
Cdd:PRK12684   3 LHQLRfVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRI-ILASVERILQEVENLK 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130715   86 KLQ---ARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRI-QAVDRQ--EDKLADDVDVAI 145
Cdd:PRK12684  82 RVGkefAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSIlQGSPTQiaEMVLHGQADLAI 147
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 11-121 1.45e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 58.13  E-value: 1.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   11 LR-VFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLL-LTEEGQSyFLDIKEIFSQLTEATRKLQ 88
Cdd:PRK12683   6 LRiIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKE-LLQIVERMLLDAENLRRLA 84

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 16130715   89 ARSAK---GALTVSLLPSFAIHWLVPRLSSFNSAYP 121
Cdd:PRK12683  85 EQFADrdsGHLTVATTHTQARYALPKVVRQFKEVFP 120
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 1.19e-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 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: 54.14  E-value: 1.19e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLL 173
Cdd:cd08479   1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKTPEDLAKHTLL----HDASRRDWqTYTRQLGLNHINVqQGPIFS-HSAMVLQAAIHGQGVALANNVMAQSEI 248
Cdd:cd08479  81 LERHGAPASPEDLARHDCLvireNDEDFGLW-RLRNGDGEATVRV-RGALSSnDGEVVLQWALDGHGIILRSEWDVAPYL 158


                ....*.
gi 16130715 249 EAGRLV 254
Cdd:cd08479 159 RSGRLV 164
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-191 1.24e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 55.00  E-value: 1.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARH-LSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLL-LTEEGQSYFLDIKEIFS------- 78
Cdd:PRK12682   3 LQQLRFVREAVRRnLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILRevgnikr 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   79 -----------QLTEATRKLQARsakgaltvSLLPsfaihwlvPRLSSFNSAYPGIDVRIQAVDRQE--DKLADDV-DVA 144
Cdd:PRK12682  83 igddfsnqdsgTLTIATTHTQAR--------YVLP--------RVVAAFRKRYPKVNLSLHQGSPDEiaRMVISGEaDIG 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 16130715  145 IFYGR-GNWPGLRVEKLYA---EYLLPVCSPllLTGEKPLkTPEDLAKHTL 191
Cdd:PRK12682 147 IATESlADDPDLATLPCYDwqhAVIVPPDHP--LAQEERI-TLEDLAEYPL 194
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-89 1.62e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.59  E-value: 1.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   11 LRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFrRRNRSLLLTEEGQSYFLDIK-------EIFSQLTEA 83
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLRHLRqvalleaDLLSTLPAE 85


                 ....*.
gi 16130715   84 TRKLQA 89
Cdd:PRK13348  86 RGSPPT 91
nhaR PRK11062
transcriptional activator NhaR; Provisional
 22-70 3.43e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 53.86  E-value: 3.43e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 16130715   22 SFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYF 70
Cdd:PRK11062  20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF 68
PRK10341 PRK10341
transcriptional regulator TdcA;
5-127 4.08e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 53.71  E-value: 4.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    5 LPPLNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEAT 84
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 16130715   85 RKLQARSAKGALTVSL-LPSFAIHWLVPR-LSSFNSAYPGIDVRI 127
Cdd:PRK10341  86 NEINGMSSEAVVDVSFgFPSLIGFTFMSDmINKFKEVFPKAQVSM 130
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 16-66 5.95e-08

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 53.11  E-value: 5.95e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 16130715   16 AAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEG 66
Cdd:PRK11151  11 ALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-145 6.59e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 52.51  E-value: 6.59e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   31 FVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL--QARSAKGALTV--------SL 100
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLdqQGPSLSGELSLfcsvtaaySH 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 16130715  101 LPsfaihwlvPRLSSFNSAYPGIDVRI------QAVDRQedkLADDVDVAI 145
Cdd:PRK11716  82 LP--------PILDRFRAEHPLVEIKLttgdaaDAVEKV---QSGEADLAI 121
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-254 1.49e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 50.92  E-value: 1.49e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 101 LPSFAIHWLV-PRLSSFNSAYPGIDVRIQAVDRQED----------KLADDVD---VAIFYGrgnwPGLRveklyaeyLL 166
Cdd:cd08474   9 APRVAARLLLaPLLARFLARYPDIRLELVVDDGLVDivaegfdagiRLGESVEkdmVAVPLG----PPLR--------MA 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 167 PVCSPLLLTGEKPLKTPEDLAKHTLL-----HDASRRDWQtYTRqlGLNHINVQ-QGP-IFSHSAMVLQAAIHGQGVALA 239
Cdd:cd08474  77 VVASPAYLARHGTPEHPRDLLNHRCIryrfpTSGALYRWE-FER--GGRELEVDvEGPlILNDSDLMLDAALDGLGIAYL 153

                       170
                ....*....|....*
gi 16130715 240 NNVMAQSEIEAGRLV 254
Cdd:cd08474 154 FEDLVAEHLASGRLV 168
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 13-257 2.66e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 51.15  E-value: 2.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   13 VFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRR-RNR------SLLLTEEGQSYFLDIKEIFSQlTEATR 85
Cdd:PRK11013  11 IFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERvRGRlhptvqGLRLFEEVQRSYYGLDRIVSA-AESLR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   86 KLQarsaKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAvdrQEDKLADDVDVAIFYGRG------NWPGLRVEK 159
Cdd:PRK11013  90 EFR----QGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVP---QESPLLEEWLSAQRHDLGltetlhTPAGTERTE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  160 LYA--EY-LLPVCSPLLltgEKPLKTPEDLAKHTLLhDASRRDwqTYtRQLgLNHINVQQG-----PIFSHSA-----MV 226
Cdd:PRK11013 163 LLTldEVcVLPAGHPLA---AKKVLTPDDFAGENFI-SLSRTD--SY-RQL-LDQLFAEHGvkrrmVVETHSAasvcaMV 234

                        250       260       270
                 ....*....|....*....|....*....|.
gi 16130715  227 LQaaihGQGVALANNVMAQSEIEAGRLVCPF 257
Cdd:PRK11013 235 RA----GVGVSIVNPLTALDYAGSGLVVRRF 261
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-67 3.39e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.54  E-value: 3.39e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 16130715   10 ALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFrRRNRSLLLTEEGQ 67
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQ 62
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-284 5.23e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 49.17  E-value: 5.23e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFaiHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLL 173
Cdd:cd08476   1 GRLRVSLPLVG--GLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKTPEDLAKHTLLHdasRR--------DWQTYTRQLGLNhINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQ 245
Cdd:cd08476  79 LARHGTPETPADLAEHACLR---YRfpttgklePWPLRGDGGDPE-LRLPTALVCNNIEALIEFALQGLGIACLPDFSVR 154

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 16130715 246 SEIEAGRLVCPFNDVLVSKNAFYLVCHDSQAELGKIAAF 284
Cdd:cd08476 155 EALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVF 193
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-67 8.67e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.25  E-value: 8.67e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 16130715   19 RHlsFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQ 67
Cdd:PRK03601  16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGE 62
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 1.23e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 48.29  E-value: 1.23e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSPLL 173
Cdd:cd08471   1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 174 LTGEKPLKTPEDLAKHTLLH---DASRRDWQTYTRQlglNHINVQQGP--IFSHSAMVLQAAIHGQGVALANNVMAQSEI 248
Cdd:cd08471  81 LARHGTPKHPDDLADHDCIAftgLSPAPEWRFREGG---KERSVRVRPrlTVNTVEAAIAAALAGLGLTRVLSYQVAEEL 157


                ....*..
gi 16130715 249 EAGRLVC 255
Cdd:cd08471 158 AAGRLQR 164
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 22-198 1.34e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 48.91  E-value: 1.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   22 SFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTeatrklQARSA--------K 93
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCE------QAQLAvhnvgqalS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   94 GALTVSLLPSFAIHWL-VPRLSSFNSAYPGIDVRIQ---AVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVC 169
Cdd:PRK11233  91 GQVSIGLAPGTAASSLtMPLLQAVRAEFPGIVLYLHensGATLNEKLMNGQLDMAVIYEHSPVAGLSSQPLLKEDLFLVG 170

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 16130715  170 splllTGEKPLKTPE--DLAKHTLL----HDASRR 198
Cdd:PRK11233 171 -----TQDCPGQSVDlaAVAQMNLFlprdYSAVRL 200
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 94-231 2.57e-06

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 47.32  E-value: 2.57e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAV--DRQEDKLADD-VDVAIFYGRGNWPGLRVEKLYAEYL-LPVC 169
Cdd:cd08425   1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMpqERIEAALADDrLDLGIAFAPVRSPDIDAQPLFDERLaLVVG 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130715 170 SPLLLTGEKPLKTPEDLA--KHTLLHD--ASRRDWQTYTRQLGL--------NHIN-----VQQGPIfshsAMVLQAAI 231
Cdd:cd08425  81 ATHPLAQRRTALTLDDLAaePLALLSPdfATRQHIDRYFQKQGIkpriaieaNSISavlevVRRGRL----ATILPDAI 155
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 9.02e-06

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 45.76  E-value: 9.02e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFaihwlvprLSSFNSAYPGI--DVRIQAV-DRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCS 170
Cdd:cd08426   8 EGLAAELLPSL--------IARFRQRYPGVffTVDVASTaDVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 171 PLLLTGEKPLKTPEDLAKHTLL--HDAS--RRDWQTYTRQLGlnhinVQQGPIF--SHSAMVLQAAIHGQGVALANNVMA 244
Cdd:cd08426  80 PGHPLARQPSVTLAQLAGYPLAlpPPSFslRQILDAAFARAG-----VQLEPVLisNSIETLKQLVAAGGGISLLTELAV 154

                       170
                ....*....|
gi 16130715 245 QSEIEAGRLV 254
Cdd:cd08426 155 RREIRRGQLV 164
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 9.12e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 45.62  E-value: 9.12e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  94 GALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAI-FYGRGNWPGLRVEKLYAEYLLPVCSPL 172
Cdd:cd08475   1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVrIGELADSTGLVARRLGTQRMVLCASPA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 173 LLTGEKPLKTPEDLAKH---TLLHDASRRDWQTYTRQLGLNHINVQQGPIFSHSAMVLQAAIHGQGVALANNVMAQSEIE 249
Cdd:cd08475  81 YLARHGTPRTLEDLAEHqciAYGRGGQPLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160


                ....*
gi 16130715 250 AGRLV 254
Cdd:cd08475 161 RGELV 165
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 96-238 1.06e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 45.19  E-value: 1.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSfAIHWLVPR-LSSFNSAYPGIDVRIQAV--DRQEDKLADD-VDVAIFYGRGNWPGLRVEKLYAEYL---LPV 168
Cdd:cd08414   2 LRIGFVGS-ALYGLLPRlLRRFRARYPDVELELREMttAEQLEALRAGrLDVGFVRPPPDPPGLASRPLLREPLvvaLPA 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130715 169 CSPllLTGEKPLkTPEDLAKHTLL----HDAS--RRDWQTYTRQLGLnHINVQQGPIFSHSAMVLQAAihGQGVAL 238
Cdd:cd08414  81 DHP--LAARESV-SLADLADEPFVlfprEPGPglYDQILALCRRAGF-TPRIVQEASDLQTLLALVAA--GLGVAL 150
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-272 1.15e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 46.22  E-value: 1.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIKEIFSQLTEATRKL 87
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715   88 QARSakGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAIFYGRGNWPGLRVEKLYAEY 164
Cdd:PRK10837  85 REDN--GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDviNAVLDfRVDIGLIEGPCHSPELISEPWLEDE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  165 LLPVCSPLLLTGEKPLkTPEDLAKHTLLhdasRRDWQTYTRQLgLNHINVQQGPIFS------HSAMVLQAAIHGQGVAL 238
Cdd:PRK10837 163 LVVFAAPDSPLARGPV-TLEQLAAAPWI----LRERGSGTREI-VDYLLLSHLPRFElamelgNSEAIKHAVRHGLGISC 236

                        250       260       270
                 ....*....|....*....|....*....|....
gi 16130715  239 ANNVMAQSEIEAGRLVCPFNDVLVSKNAFYLVCH 272
Cdd:PRK10837 237 LSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHH 270
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-254 5.85e-05

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: 43.07  E-value: 5.85e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 109 LVPRLSSFNSAYPGIDVRIQAVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLyAEYLLPVC-SPLLLTGEKPLKTPEDLA 187
Cdd:cd08470  16 IAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRL-ASRRHYVCaSPAYLERHGTPHSLADLD 94

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130715 188 KHTLLHdASRRDWQtyTRQLGLNHINVQQGPIFSHS-AMVLQAAIHGQGVALANNVMAQSEIEAGRLV 254
Cdd:cd08470  95 RHNCLL-GTSDHWR--FQENGRERSVRVQGRWRCNSgVALLDAALKGMGLAQLPDYYVDEHLAAGRLV 159
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-193 1.45e-04

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 42.13  E-value: 1.45e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQ---EDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVC--- 169
Cdd:cd08440   2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEqviEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCpkd 81

                        90       100
                ....*....|....*....|....
gi 16130715 170 SPLlltGEKPLKTPEDLAKHTLLH 193
Cdd:cd08440  82 HPL---ARRRSVTWAELAGYPLIA 102
cysB PRK12681
HTH-type transcriptional regulator CysB;
8-145 5.08e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 41.04  E-value: 5.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715    8 LNALRVFDAAARH-LSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLL-LTEEGQSYFLDIKEIFSQlTEATR 85
Cdd:PRK12681   3 LQQLRYIVEVVNHnLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSK-VESIK 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130715   86 KL---QARSAKGALTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRI-QAVDRQ-EDKLAD-DVDVAI 145
Cdd:PRK12681  82 SVageHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMhQGSPTQiAEAAAKgNADFAI 147
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-238 5.46e-04

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 40.27  E-value: 5.46e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQAVDRQE--DKLAD-DVDVAI-----FYGRGNWPGLRVEKLYAEYL-- 165
Cdd:cd08423   2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPEslDALRAgELDLAVvfdypVTPPPDDPGLTRVPLLDDPLdl 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715 166 -LPVCSPLlltGEKPLKTPEDLAKHTLLHDASRRDWQTYTRQLGLnhinvQQG--PIFSHSA----MVLQAAIHGQGVAL 238
Cdd:cd08423  82 vLPADHPL---AGREEVALADLADEPWIAGCPGSPCHRWLVRACR-----AAGftPRIAHEAddyaTVLALVAAGLGVAL 153
leuO PRK09508
leucine transcriptional activator; Reviewed
 8-58 6.87e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 37.69  E-value: 6.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 16130715    8 LNALRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNR 58
Cdd:PRK09508  24 LNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGR 74
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 96-192 8.58e-03

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 36.80  E-value: 8.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130715  96 LTVSLLPSFAIHWLVPRLSSFNSAYPGIDVRIQ---AVDRQEDKLADDVDVAIFYGRGNWPGLRVEKLYAEYLLPVCSP- 171
Cdd:cd08433   2 VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVeglSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPAd 81

                        90       100
                ....*....|....*....|.
gi 16130715 172 LLLTGEKPLkTPEDLAKHTLL 192
Cdd:cd08433  82 APLPRGAPV-PLAELARLPLI 101
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
11-74 9.54e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 36.96  E-value: 9.54e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16130715   11 LRVFDAAARHLSFTRAAEELFVTQAAVSHQIKSLEDFLGLKLFRRRNRSLLLTEEGQSYFLDIK 74
Cdd:PRK15243   9 LKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVK 72
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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