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Conserved domains on  [gi|727162673|ref|WP_033634950|]
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MULTISPECIES: HTH-type transcriptional regulator Cbl [Serratia]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
cbl super family cl32803
HTH-type transcriptional regulator Cbl;
1-317 0e+00

HTH-type transcriptional regulator Cbl;


The actual alignment was detected with superfamily member PRK12679:

Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 539.40  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12679   1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAERILNEASNV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12679 161 FPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSLTEIKDKVFSSQlDAVIDYQI 317
Cdd:PRK12679 241 GLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVMENS-EEEIDYQI 316
 
Name Accession Description Interval E-value
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-317 0e+00

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 539.40  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12679   1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAERILNEASNV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12679 161 FPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSLTEIKDKVFSSQlDAVIDYQI 317
Cdd:PRK12679 241 GLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVMENS-EEEIDYQI 316
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
94-291 3.89e-111

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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. 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 320.34  E-value: 3.89e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVTLPCYRWNHCVIVP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERD 253
Cdd:cd08413   81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRD 160
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 727162673 254 RGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:cd08413  161 ADLVALDAGHLFGPNTTRIALRRGTYLRSYAYDFIELF 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
92-291 1.11e-40

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: 140.89  E-value: 1.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   92 SGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLAAFPYYRWHHTIL 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP-DDPGLEARPLGEEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  172 VPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKE 251
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 727162673  252 RDRG-LVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:pfam03466 160 LADGrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.86e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 135.76  E-value: 3.86e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNyNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILNDANNI 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEG-SFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLR-LTEAGERLLERARRILAELEEA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLAA 160
Cdd:COG0583   79 EAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPP-PDPGLVA 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTlemlstlplityrqgitgrakldaafkaagltpdialsaQDSDVIKTYVELGLGV 240
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAGLGI 198
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 727162673 241 GVLADMSYEKERDRG-LVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:COG0583  199 ALLPRFLAADELAAGrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-317 0e+00

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 539.40  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12679   1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAERILNEASNV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12679 161 FPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSLTEIKDKVFSSQlDAVIDYQI 317
Cdd:PRK12679 241 GLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVMENS-EEEIDYQI 316
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
1-308 0e+00

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 522.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12682   1 MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERILREVGNI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12682  81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLAT 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12682 161 LPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGV 240
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSLTEIKDKVFSSQ 308
Cdd:PRK12682 241 GIVAEMAYRPDRDGDLVALPAGHLFGPNTAWVALKRGAYLRNYVYKFIELCAPHLSRELIKRAVQGDN 308
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
1-307 2.11e-177

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 492.64  E-value: 2.11e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12683   1 MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVS 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12683 161 FPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGV 240
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSLTEIKDKVFSS 307
Cdd:PRK12683 241 GIVAAMAYDPQRDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPHLSEAEIAAALREA 307
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-295 1.76e-140

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 399.35  E-value: 1.76e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12684   1 MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERILQEVENL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12684  81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKELVS 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12684 161 LPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLGV 240
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTL 295
Cdd:PRK12684 241 GIVADMAFDPERDRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPTL 295
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
94-291 3.89e-111

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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. 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 320.34  E-value: 3.89e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVTLPCYRWNHCVIVP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERD 253
Cdd:cd08413   81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRD 160
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 727162673 254 RGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:cd08413  161 ADLVALDAGHLFGPNTTRIALRRGTYLRSYAYDFIELF 198
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-304 2.43e-108

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 318.00  E-value: 2.43e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVESI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLYDDLIM 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:PRK12681 161 LPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727162673 241 GVLADMSYEKERDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSlteiKDKV 304
Cdd:PRK12681 241 GVIASMAVDPVADPDLVAIDASHLFSHSTTKIGFRRGTFLRSYMYDFIERFAPHLT----RDVV 300
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
94-291 4.95e-105

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl 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. 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 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: 176135  Cd Length: 198  Bit Score: 305.20  E-value: 4.95e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08444    1 ELTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELVSFPYYDWHHHIIVP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERD 253
Cdd:cd08444   81 VGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRD 160
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 727162673 254 RGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:cd08444  161 TNLIKLDTSHLFGKNTTWIALRRGGDLRNFAYRFIELC 198
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
94-290 1.13e-68

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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. 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 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: 176134  Cd Length: 198  Bit Score: 212.81  E-value: 1.13e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08443    1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLITLPCYHWNRCVVVK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERD 253
Cdd:cd08443   81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDD 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 727162673 254 RGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQL 290
Cdd:cd08443  161 PDLVIRDARDLFPWSVTKIAFRRGTFLRSYMYDFIQR 197
PRK12680 PRK12680
LysR family transcriptional regulator;
1-301 6.43e-58

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 189.45  E-value: 6.43e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNI 80
Cdd:PRK12680   1 MTLTQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGVEVIERARAVLSEANNI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAA 160
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRqPQVTLEM--LSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGL 238
Cdd:PRK12680 161 VPLYRWRRLVVVPRGHALDT-PRRAPDMaaLAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGL 239
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727162673 239 GVGVLADMSYEKErDRGLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPTLSLTEIK 301
Cdd:PRK12680 240 GVGLLAEMAVNAN-DEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALELVHVLAPQIDKRDLR 301
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
92-291 1.11e-40

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: 140.89  E-value: 1.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   92 SGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLAAFPYYRWHHTIL 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP-DDPGLEARPLGEEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  172 VPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKE 251
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 727162673  252 RDRG-LVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:pfam03466 160 LADGrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
95-291 4.83e-39

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: 136.19  E-value: 4.83e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  95 LHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLAAFPYYRWHHTILVPE 174
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPV-DDPGLESEPLFEEPLVLVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 175 GHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERDR 254
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 727162673 255 GLVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.86e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 135.76  E-value: 3.86e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNyNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILNDANNI 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEG-SFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLR-LTEAGERLLERARRILAELEEA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLAA 160
Cdd:COG0583   79 EAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPP-PDPGLVA 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 161 FPYYRWHHTILVPEGHELTRQPQVTlemlstlplityrqgitgrakldaafkaagltpdialsaQDSDVIKTYVELGLGV 240
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAGLGI 198
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 727162673 241 GVLADMSYEKERDRG-LVSLNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:COG0583  199 ALLPRFLAADELAAGrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
94-246 4.22e-32

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong 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: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 118.02  E-value: 4.22e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDEsLAAFPYYRWHHTILVP 173
Cdd:cd08434    1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPD-IEWIPLFTEELVLVVP 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADM 246
Cdd:cd08434   80 KDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEM 152
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
95-258 1.02e-28

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 109.19  E-value: 1.02e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  95 LHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLAAFPYYRWHHTILVPE 174
Cdd:cd08415    2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPL-DHPGLESEPLASGRAVCVLPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 175 GHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERDR 254
Cdd:cd08415   81 GHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAGA 160

                 ....
gi 727162673 255 GLVS 258
Cdd:cd08415  161 GLVV 164
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-259 5.06e-26

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: 102.22  E-value: 5.06e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERlMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEP-EADPDLEFEPLLRDPFVLVCP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSA-QDSDVIkTYVELGLGVGVLADMSYEKER 252
Cdd:cd08440   80 KDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVsHMSTAL-GMVAAGLGVAVLPALALPLAD 158

                 ....*..
gi 727162673 253 DRGLVSL 259
Cdd:cd08440  159 HPGLVAR 165
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
94-264 1.62e-24

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: 98.33  E-value: 1.62e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAsERLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLV-EGPVDHPDLIVEPFAEDELVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPD---IALSAQDSDVIKTYVELGLGVGVLADMSYEK 250
Cdd:cd08420   80 PDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLdlnIVMELGSTEAIKEAVEAGLGISILSRLAVRK 159
                        170
                 ....*....|....*
gi 727162673 251 ERDRG-LVSLNAEHL 264
Cdd:cd08420  160 ELELGrLVALPVEGL 174
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
94-243 4.32e-24

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: 96.81  E-value: 4.32e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAseRL-MSDESLAAFPYYRWHHTILV 172
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFV--RPpPDPPGLASRPLLREPLVVAL 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727162673 173 PEGHELTRQPQVTLEMLSTLPLITYRQGITG--RAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL 243
Cdd:cd08414   79 PADHPLAARESVSLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALV 151
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-243 2.94e-22

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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 91.89  E-value: 2.94e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAS--ERLMsdESLAAFPYYRWHHTIL 171
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGlpERRP--PGLASRELAREPLVAV 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727162673 172 VPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL 243
Cdd:cd08436   79 VAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALL 150
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
94-291 4.16e-22

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 91.84  E-value: 4.16e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIA-SERLMSD---ESLAAFPYYRWhht 169
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTyDLDLPEDiafEPLARLPPYVW--- 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 170 ilVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDaAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL-----A 244
Cdd:cd08412   78 --LPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFLS-LFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLndrpyR 154
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 727162673 245 DMSYEKERdrgLVSLN-AEHLFEPNTVWLGLKRSQLqRNYAWRFIQLC 291
Cdd:cd08412  155 PWSYDGKR---LVRRPlADPVPPLRLGLAWRRGARL-TRAARAFVDFA 198
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-246 7.15e-22

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: 91.12  E-value: 7.15e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  95 LHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASErlMSDESLAAFPYYRWHH------ 168
Cdd:cd08423    2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFD--YPVTPPPDDPGLTRVPllddpl 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727162673 169 TILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADM 246
Cdd:cd08423   80 DLVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRL 157
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-255 2.48e-20

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: 86.98  E-value: 2.48e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASerlmsdeSLAAFPYYRWHHT------ILVPEGHELTRQ 181
Cdd:cd08426   15 LPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAF-------SPPPEPGIRVHSRqpapigAVVPPGHPLARQ 87
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727162673 182 PQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERDRG 255
Cdd:cd08426   88 PSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRG 161
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
94-264 1.54e-18

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 81.78  E-value: 1.54e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTqARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASeRLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08419    1 RLRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMG-RPPEDLDLVAEPFLDNPLVVIAP 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKE-R 252
Cdd:cd08419   79 PDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALElA 158
                        170
                 ....*....|..
gi 727162673 253 DRGLVSLNAEHL 264
Cdd:cd08419  159 TGRLAVLDVEGF 170
rbcR CHL00180
LysR transcriptional regulator; Provisional
4-258 3.62e-18

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 83.15  E-value: 3.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   4 QQLKIIRESARcNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILNDANNIRRL 83
Cdd:CHL00180   8 DQLRILKAIAT-EGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKAS-LTEAGELLLRYGNRILALCEETCRA 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  84 ADVFSSNDSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSD--ESLAAF 161
Cdd:CHL00180  86 LEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTElkKILEIT 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 162 PYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPD---IALSAQDSDVIKTYVELGL 238
Cdd:CHL00180 166 PYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKrfkIEMELNSIEAIKNAVQSGL 245
                        250       260
                 ....*....|....*....|
gi 727162673 239 GVGVLADMSYEKERDRGLVS 258
Cdd:CHL00180 246 GAAFVSVSAIEKELELGLLH 265
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
94-257 3.28e-16

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 75.53  E-value: 3.28e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASErLMSDESLAAFPYYRWHHTILVP 173
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVST-LHEPPGIERERLLRIDGVCVLP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERD 253
Cdd:cd08456   80 PGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAA 159

                 ....
gi 727162673 254 RGLV 257
Cdd:cd08456  160 AGLV 163
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
108-291 3.71e-15

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 72.59  E-value: 3.71e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERlMSDESLAAFPYYRWHHTILVPEGHELTRQPQVTLE 187
Cdd:cd08438   15 FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP-VDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 188 MLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIAL-SAQdSDVIKTYVELGLGVGVLADMSYEKERDRGLVSLnaeHLFE 266
Cdd:cd08438   94 DLADEPFILFNEDFALHDRIIDACQQAGFTPNIAArSSQ-WDFIAELVAAGLGVALLPRSIAQRLDNAGVKVI---PLTD 169
                        170       180
                 ....*....|....*....|....*...
gi 727162673 267 PNTVW-LGL--KRSQLQRNYAWRFIQLC 291
Cdd:cd08438  170 PDLRWqLALiwRKGRYLSHAARAWLALL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
18-248 4.62e-15

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 73.99  E-value: 4.62e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  18 NLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRgKRLLGMTEPGKELLVVAERILNDANNIRRLADVFSSNDSGQLHI 97
Cdd:PRK09986  23 HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRH-SRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEAGRIEI 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  98 ATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIasERLMSDESLAAFPYYRWH-HTILV--PE 174
Cdd:PRK09986 102 GIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGI--WRMADLEPNPGFTSRRLHeSAFAVavPE 179
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727162673 175 GHELTRQPQVTLEMLSTLPLITYRQGITGRAK-LDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADmSY 248
Cdd:PRK09986 180 EHPLASRSSVPLKALRNEYFITLPFVHSDWGKfLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGITLLPD-SY 253
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
18-224 8.08e-15

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 73.45  E-value: 8.08e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  18 NLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGkRLLGMTEPGKELLVVAERILNDANNIRR-LADVfSSNDSGQLH 96
Cdd:PRK11242  17 NFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSG-RTVRLTDAGEVYLRYARRALQDLEAGRRaIHDV-ADLSRGSLR 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  97 IATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIA----------SERLMsDESLAafpyyrw 166
Cdd:PRK11242  95 LAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAfapvhspeieAQPLF-TETLA------- 166
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 727162673 167 hhtILVPEGHELTRQPQ-VTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSA 224
Cdd:PRK11242 167 ---LVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEA 222
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-243 9.65e-15

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: 176113  Cd Length: 198  Bit Score: 71.40  E-value: 9.65e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMsDESLAAFPYYRWHHTILVPEGHELTRQPQVTLE 187
Cdd:cd08421   15 LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVD-AAGLETRPYRTDRLVVVVPRDHPLAGRASVAFA 93
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727162673 188 MLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL 243
Cdd:cd08421   94 DTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIV 149
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
20-294 5.02e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 71.26  E-value: 5.02e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  20 TEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILNDANNIRRLadvFSsNDSGQLHIAT 99
Cdd:PRK10837  21 TQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLV-VNEHGRLLYPRALALLEQAVEIEQL---FR-EDNGALRIYA 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 100 THTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDEsLAAFPYYRWHHTILVPEGHELT 179
Cdd:PRK10837  96 SSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPE-LISEPWLEDELVVFAAPDSPLA 174
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 180 RQPqVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERDRG-LVS 258
Cdd:PRK10837 175 RGP-VTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGISCLSRRVIADQLQAGtLVE 253
                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 727162673 259 LNAEHLFEPNTVWLGLKRSQLQRNYAWRFIQLCNPT 294
Cdd:PRK10837 254 VAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQEA 289
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-245 5.72e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 70.62  E-value: 5.72e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  29 SQSGVSRHIRELEEELGIEIFIR--RGKRLlgmTEPGKELLVVAERILNDANNIRRLADVFSSNDSGQLHIATTHTqARY 106
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRdnRSVTL---TEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVT-AAY 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 107 S-LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIA--SERLMSD---ESLAAFPYyrwhhTILVPEGH---- 176
Cdd:PRK11716  80 ShLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAakPETLPASvafSPIDEIPL-----VLIAPALPcpvr 154
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727162673 177 ELTRQPQVTlemLSTLPLITYRQGiTGRAKLDAAFKAAGLTPDIalSAQDS--DVIKTYVELGLGVGVLAD 245
Cdd:PRK11716 155 QQLSQEKPD---WSRIPFILPEHG-PARRRIDLWFRRHKIKPNI--YATVSghEAIVSMVALGCGVGLLPE 219
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
94-218 6.18e-14

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 69.22  E-value: 6.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAseRLMSDESLAAFPYYRWHH---TI 170
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIG--RLADDEQPPDLASEELADeplVV 78
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 727162673 171 LVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTP 218
Cdd:cd08435   79 VARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPL 126
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
97-244 1.96e-13

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: 68.01  E-value: 1.96e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  97 IATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERlMSDESLAAFPYYRWHHTILVPEGH 176
Cdd:cd08433    4 VGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGP-PPIPGLSTEPLLEEDLFLVGPADA 82
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727162673 177 ELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLA 244
Cdd:cd08433   83 PLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILP 150
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
94-291 8.95e-13

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 66.05  E-value: 8.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATT-HTQARYSLPgVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDEsLAAFPYYRWHHTILV 172
Cdd:cd08441    1 RLRIAVEcHSCFDWLMP-VLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPG-IAYEPLFDYEVVLVV 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 173 PEGHELTRQPQVTLEMLSTLPLITYRqgiTGRAKLDAA---FKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYE 249
Cdd:cd08441   79 APDHPLAAKEFITPEDLADETLITYP---VERERLDVFrhfLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVR 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 727162673 250 KERDRGLVS---LNAEHLFEpnTVWLGLKRSQLQRNYAWRFIQLC 291
Cdd:cd08441  156 EYLDQGLVVarpLGEEGLWR--TLYAAVRTEDADQPYLQDFLELA 198
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
94-257 1.23e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 65.37  E-value: 1.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIA-SERLMSDESLAAFPYYRWHHTILV 172
Cdd:cd08449    1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrFADTLNDPPLASELLWREPMVVAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 173 PEGHELTRQPQVTLEMLSTLPLITYRQGITGRAK-LDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADmSYEKE 251
Cdd:cd08449   81 PEEHPLAGRKSLTLADLRDEPFVFLRLANSRFADfLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPE-SYARL 159

                 ....*.
gi 727162673 252 RDRGLV 257
Cdd:cd08449  160 PWPGVR 165
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
18-257 1.98e-12

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 66.55  E-value: 1.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  18 NLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRL------LGMTEPGKELLVVAERILNDANNIRRLADvfssnd 91
Cdd:PRK11013  20 SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLhptvqgLRLFEEVQRSYYGLDRIVSAAESLREFRQ------ 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  92 sGQLHIATTHTQARYSLPGVIKEFRALYPRVRV-VLNQGSP--EEivsMLAAGEADIGIAserlmsdESLAAFPYYRWHH 168
Cdd:PRK11013  94 -GQLSIACLPVFSQSLLPGLCQPFLARYPDVSLnIVPQESPllEE---WLSAQRHDLGLT-------ETLHTPAGTERTE 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 169 TILV------PEGHELTRQPQVTLEMLSTLPLI------TYRQgitgraKLDAAFKAAGLTPDIALSAQDSDVIKTYVEL 236
Cdd:PRK11013 163 LLTLdevcvlPAGHPLAAKKVLTPDDFAGENFIslsrtdSYRQ------LLDQLFAEHGVKRRMVVETHSAASVCAMVRA 236
                        250       260
                 ....*....|....*....|.
gi 727162673 237 GLGVGVLADMSYEKERDRGLV 257
Cdd:PRK11013 237 GVGVSIVNPLTALDYAGSGLV 257
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
95-258 2.37e-12

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 64.82  E-value: 2.37e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  95 LHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAS----ERLMSDESLAAFPYyrwhhTI 170
Cdd:cd08457    2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADgpleERQGFLIETRSLPA-----VV 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 171 LVPEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEK 250
Cdd:cd08457   77 AVPMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIG 156

                 ....*...
gi 727162673 251 ERDRGLVS 258
Cdd:cd08457  157 LPLDGIVI 164
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
104-243 8.75e-12

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 62.98  E-value: 8.75e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 104 ARYS-LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAS--ERLMSD---ESLAAFPYyrwhhTILVPEGHE 177
Cdd:cd08430   10 ASYSfLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAArpDKLPARlafLPLATSPL-----VFIAPNIAC 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727162673 178 LTRQPQVTLEM-LSTLPLITYRQGITgRAKLDAAFKAAGLTPDIalSAQDS--DVIKTYVELGLGVGVL 243
Cdd:cd08430   85 AVTQQLSQGEIdWSRLPFILPERGLA-RERLDQWFRRRGIKPNI--YAQVAghEAIVSMVALGCGVGIV 150
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
93-224 5.97e-11

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: 60.81  E-value: 5.97e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  93 GQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDEsLAAFPYYRWHHTILV 172
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPD-IDAQPLFDERLALVV 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 727162673 173 PEGHELTRQPQV-TLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSA 224
Cdd:cd08425   80 GATHPLAQRRTAlTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEA 132
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
93-196 2.22e-10

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR 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. 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 59.08  E-value: 2.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  93 GQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASeRLMSDESLAAFPYYRWHHTILV 172
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLA-LPVDEPGLEEEPLFDEPFLLAV 79
                         90       100
                 ....*....|....*....|....
gi 727162673 173 PEGHELTRQPQVTLEMLSTLPLIT 196
Cdd:cd08411   80 PKDHPLAKRKSVTPEDLAGERLLL 103
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-240 1.79e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 56.51  E-value: 1.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDEsLAAFPYYRWHHTILVPEGHELTRQPQVTLE 187
Cdd:cd08448   15 LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAG-LSARLLHREPFVCCLPAGHPLAARRRIDLR 93
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727162673 188 MLSTLPLI--------TYRQGITgrakldAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:cd08448   94 ELAGEPFVlfsrevspDYYDQII------ALCMDAGFHPKIRHEVRHWLTVVALVAAGMGV 148
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
94-225 3.18e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 55.68  E-value: 3.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDEsLAAFPYYRWHHTILVP 173
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPG-LRSQPLFEDRFVCVAR 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 727162673 174 EGHELTRQPqVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQ 225
Cdd:cd08417   80 KDHPLAGGP-LTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVP 130
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
94-240 3.48e-09

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 55.65  E-value: 3.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSL-PGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADI-----------GIASERLMSDESLAAf 161
Cdd:cd08451    1 RLRVGFTSSAAFHPLvPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAafvrppvarsdGLVLELLLEEPMLVA- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 162 pyyrwhhtilVPEGHELTRQPQVTLEMLSTLPLITYRQGItGRAKLD---AAFKAAGLTPDIalsAQDSDVIKTYVEL-- 236
Cdd:cd08451   80 ----------LPAGHPLARERSIPLAALADEPFILFPRPV-GPGLYDaiiAACRRAGFTPRI---GQEAPQMASAINLva 145

                 ....*
gi 727162673 237 -GLGV 240
Cdd:cd08451  146 aGLGV 150
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
104-240 7.46e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 54.67  E-value: 7.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 104 ARYS-LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIG--IASERLMSDESLAAFPYYRWHHTILVPEGHELTR 180
Cdd:cd08453   10 ADYSvLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGivIPPPGASAPPALAYRPLLSEPLVLAVPAAWAAEG 89
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727162673 181 QPQVTLEMLSTLPLITYRQGITgRAKLDA---AFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:cd08453   90 GAPLALAAVAAEPLVIFPRRIA-PAFHDAvtgYYRAAGQTPRIAQEAIQMQTIISLVSAGMGV 151
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
93-240 8.05e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 54.59  E-value: 8.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  93 GQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIG----------IASERLmSDESLaafp 162
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGfgrfypvepdIAVENV-AQERL---- 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 163 yyrwhhTILVPEGHELTRQPQVTLEMLSTLPLITYRQGitGRA----KLDAAFKAAGLTPDIALSAQDSDVIKTYVELGL 238
Cdd:cd08446   76 ------YLAVPKSHPLAARPAVSLADLRNEPLILFPRG--GRPsfadEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGF 147

                 ..
gi 727162673 239 GV 240
Cdd:cd08446  148 GV 149
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-245 1.65e-08

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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 53.73  E-value: 1.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  95 LHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASE---RLMSDesLAAFPYYRWHHTIL 171
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEppfPLPKD--LVWTPLVREPLVLI 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727162673 172 VPEGHELTRqpqvTLEMLSTLPLITY-RQGITGRaKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLAD 245
Cdd:cd08427   80 APAELAGDD----PRELLATQPFIRYdRSAWGGR-LVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPD 149
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
23-254 8.09e-08

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 52.72  E-value: 8.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  23 ANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILNDANNIRRLADVFSSNDSGQLHIATTHT 102
Cdd:PRK11151  22 ADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVL-FTQAGLLLVDQARTVLREVKVLKEMASQQGETMSGPLHIGLIPT 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 103 QARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIaserLMSDESLAAF---PYYRWHHTILVPEGHELT 179
Cdd:PRK11151 101 VGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI----LALVKESEAFievPLFDEPMLLAVYEDHPWA 176
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 180 RQPQVTLEMLSTLPLITYRQGITGR-----------AKLDAAFKAAGLtpdialsaqdsDVIKTYVELGLGVGVLADMSY 248
Cdd:PRK11151 177 NRDRVPMSDLAGEKLLMLEDGHCLRdqamgfcfeagADEDTHFRATSL-----------ETLRNMVAAGSGITLLPALAV 245

                 ....*.
gi 727162673 249 EKERDR 254
Cdd:PRK11151 246 PNERKR 251
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
104-243 1.01e-07

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 51.35  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 104 ARYS-LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSdESLAAFPYYRWHHTILVPEGHELTRQP 182
Cdd:cd08452   10 AIYEfLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQH-TALHIETVQSSPCVLALPKQHPLASKE 88
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727162673 183 QVTLEMLSTLPLITYRQGITGRAKLD--AAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL 243
Cdd:cd08452   89 EITIEDLRDEPIITVAREAWPTLYDEiiQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFV 151
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
18-243 3.65e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.92  E-value: 3.65e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  18 NLTEVANTLFTSQSGVSRHIRELEeELGIEIFIRRGKRLLGMTEPGKELLVVAERILNDANNIRRLADVFSSNDSgQLHI 97
Cdd:PRK09906  17 NFTKAAEKLHTAQPSLSQQIKDLE-NCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQEDR-QLTI 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  98 ATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLMSDESLAAF----PYyrwhhTILVP 173
Cdd:PRK09906  95 GFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLElldePL-----VVVLP 169
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLIT--YRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL 243
Cdd:PRK09906 170 VDHPLAHEKEITAAQLDGVNFIStdPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCTII 241
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
106-222 5.79e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 49.11  E-value: 5.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 106 YSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADI----------GIASERLMSDeslaafpyyrwHHTILVPEG 175
Cdd:cd08459   13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLaigylpdlgaGFFQQRLFRE-----------RYVCLVRKD 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 727162673 176 HELTRQPqVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIAL 222
Cdd:cd08459   82 HPRIGST-LTLEQFLAARHVVVSASGTGHGLVEQALREAGIRRRIAL 127
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-257 8.50e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 49.63  E-value: 8.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   1 MNFQQLKIIRESARCNyNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILndaNNI 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLANQVL---PQI 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  81 RRLADVFSSNDSGQLHIAT-THTQARYSLPGvIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASErLMSDESLA 159
Cdd:PRK15421  77 SQALQACNEPQQTRLRIAIeCHSCIQWLTPA-LENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSD-ILPRSGLH 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 160 AFPYYRWHHTILVPEGHELTRQPQVTLEMLSTLPLITYRqgiTGRAKLDA---AFKAAGLTPDIAlSAQDSDVIKTYVEL 236
Cdd:PRK15421 155 YSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYP---VQRSRLDVwrhFLQPAGVSPSLK-SVDNTLLLIQMVAA 230
                        250       260
                 ....*....|....*....|.
gi 727162673 237 GLGVGVLADMSYEKERDRGLV 257
Cdd:PRK15421 231 RMGIAALPHWVVESFERQGLV 251
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-235 1.47e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 48.05  E-value: 1.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASeRLMSDESLAAFPYYRWHHTILVPEGHELTRQPqVTLE 187
Cdd:cd08461   15 LPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTT-PEYAPDGLRSRPLFEERYVCVTRRGHPLLQGP-LSLD 92
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 727162673 188 MLSTLPLITYRQGITG-RAKLDAAFKAAGLTPDIALSAQDSDVIKTYVE 235
Cdd:cd08461   93 QFCALDHIVVSPSGGGfAGSTDEALAALGLTRNVVLSVPSFLVVPEILA 141
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
106-240 1.59e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 48.03  E-value: 1.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 106 YS-LPGVIKEFRALYPRVRVVLnqgspEEIVSM-----LAAGEADIG----------IASERLMSDESLAAfpyyrwhht 169
Cdd:cd08447   12 YSfLPRLLAAARAALPDVDLVL-----REMVTTdqieaLESGRIDLGllrppfarpgLETRPLVREPLVAA--------- 77
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 727162673 170 ilVPEGHELTRQPQVTLEMLSTLPLITYRqgiTGRAK-----LDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGV 240
Cdd:cd08447   78 --VPAGHPLAGAERLTLEDLDGQPFIMYS---PTEARyfhdlVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGV 148
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
95-257 2.14e-06

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 47.40  E-value: 2.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  95 LHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIAseRLMSD-ESLAAFPYYRWHHTILVP 173
Cdd:cd08458    2 LRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGIS--ILAGDyPGLTTEPVPSFRAVCLLP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 EGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSYEKERD 253
Cdd:cd08458   80 PGHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVDPFTADYYSA 159

                 ....
gi 727162673 254 RGLV 257
Cdd:cd08458  160 NPVI 163
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-223 3.68e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 43.76  E-value: 3.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERlmsdeslaafPYYRWHHT-ILVPEGHELTRQPQ--- 183
Cdd:cd08464   15 APPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFG----------ELPAWLKReVLYTEGYACLFDPQqls 84
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 727162673 184 ----VTLEMLSTLP--LITYRQGITGraKLDAAFKAAGLTPDIALS 223
Cdd:cd08464   85 lsapLTLEDYVARPhvLVSYRGGLRG--FVDDALAELGRSRRVVAS 128
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
94-243 5.22e-05

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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. 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: 176108  Cd Length: 199  Bit Score: 43.49  E-value: 5.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  94 QLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEAD-IGIASERLMSDESLAAFPYYRWHHTILV 172
Cdd:cd08416    1 RLRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDaILVATPEGLNDPDFEVVPLFEDDIFLAV 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727162673 173 PEGHELTRQPQVTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVL 243
Cdd:cd08416   81 PATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALL 151
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
23-154 1.20e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 43.09  E-value: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  23 ANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERIL--NDanniRRLADVFSSNDSGQLHIATT 100
Cdd:PRK15092  32 AAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKL-LTEHGIQLLGYARKILrfND----EACSSLMYSNLQGVLTIGAS 106
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 727162673 101 HTQARYSLPGVIKEFRALYPR----VRVVLNQgspeEIVSMLAAGEADIGIASERLMS 154
Cdd:PRK15092 107 DDTADTILPFLLNRVSSVYPKlaldVRVKRNA----FMMEMLESQEVDLAVTTHRPSS 160
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
108-197 1.62e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 41.83  E-value: 1.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 108 LPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASERLmSDESLaafpyyrwHHTIL--------VPEGHELT 179
Cdd:cd08445   16 LPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRI-EDPAI--------RRIVLreeplvvaLPAGHPLA 86
                         90
                 ....*....|....*....
gi 727162673 180 RQPQ-VTLEMLSTLPLITY 197
Cdd:cd08445   87 QEKApLTLAQLADEPLILY 105
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
93-272 2.25e-04

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: 41.66  E-value: 2.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  93 GQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGspEEIVSMLAAGeADIGIaseRL--MSDESLAAFPYYRWHHtI 170
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLS--DRLVDLVEEG-FDLAI---RIgeLPDSSLVARRLGPVRR-V 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 171 LV--PE-----GheltrQPQvTLEMLSTLPLITYRQGITGRA-KLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGV 242
Cdd:cd08422   74 LVasPAylarhG-----TPQ-TPEDLARHRCLGYRLPGRPLRwRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIAL 147
                        170       180       190
                 ....*....|....*....|....*....|.
gi 727162673 243 LADMSYEKERDRG-LVSLNAEHLFEPNTVWL 272
Cdd:cd08422  148 LPDFLVAEDLASGrLVRVLPDWRPPPLPIYA 178
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
106-247 4.32e-04

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 40.78  E-value: 4.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 106 YSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIG--IASERLMSDEsLAAFPYYRWHHTILVPEGHELTRQPQ 183
Cdd:cd08437   13 YYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAllGSLTPLENSA-LHSKIIKTQHFMIIVSKDHPLAKAKK 91
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727162673 184 VTLEMLSTLPLITYRQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMS 247
Cdd:cd08437   92 VNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIA 155
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
18-267 7.55e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 40.81  E-value: 7.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  18 NLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRlLGMTEPGKELLVVAERILNDANNirRLADVFSSNDSGQ--L 95
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTP-LQLSEQGKIFHSQIRHLLQQLES--NLAELRGGSDYAQrkI 103
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673  96 HIATTHTQARYSLPGVIKEFRALYPRVRVVLNQgspEEIVSMLAAGEADIgIASerlMSDESL--AAFPYYRWHHTILVP 173
Cdd:PRK10082 104 KIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDV---DEAVDKLREGQSDC-IFS---FHDEDLleAPFDHIRLFESQLFP 176
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 174 ----EGHEltrQPQVTLEMlSTLPLITY-RQGITGRAKLDAAFKAAGLTPDIALSAQDSDVIKTYVELGLGVGVLADMSY 248
Cdd:PRK10082 177 vcasDEHG---EALFNLAQ-PHFPLLNYsRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGCGIAWLPEYAI 252
                        250       260
                 ....*....|....*....|
gi 727162673 249 EKE-RDRGLVSLNAEHLFEP 267
Cdd:PRK10082 253 QQEiRSGQLVVLNRDELVIP 272
PRK09791 PRK09791
LysR family transcriptional regulator;
3-147 1.09e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 40.13  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673   3 FQQLKIIRESARcNYNLTEVANTLFTSQSGVSRHIRELEEELGIEIFIRRGKRLLgMTEPGKELLVVAERILND----AN 78
Cdd:PRK09791   7 IHQIRAFVEVAR-QGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVT-LTDAGESFYQHASLILEElraaQE 84
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727162673  79 NIR-RLADVfssndSGQLHIATTHTQARYSLPGVIKEFRALYPRVRVVLNQGspeEIVSM---LAAGEADIGI 147
Cdd:PRK09791  85 DIRqRQGQL-----AGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEG---QLVSMineLRQGELDFTI 149
PBP2_phosphate_like_1 cd13653
Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 ...
112-161 5.77e-03

Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily; This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts 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. The PstS proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270371 [Multi-domain]  Cd Length: 240  Bit Score: 37.55  E-value: 5.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 727162673 112 IKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIASeRLMSDESLAAF 161
Cdd:cd13653   20 AEAFMEKHPGVRIEVQGGGSGTGIKALIEGTADIGMAS-RPLKAEEKAAA 68
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
104-237 7.86e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 36.95  E-value: 7.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 104 ARYSLPGVIKEFRALYPRVRVVLNQGSPEEIVSMLAAGEADIGIA------------SERLMSDESlaafpyyrwhhTIL 171
Cdd:cd08418   11 AHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGtlpdemylkeliSEPLFESDF-----------VVV 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727162673 172 VPEGHELTRQPqvTLEMLS----TLPliTYRQGiTGRAKLDaAFKAAGLTPDIALSAQDSDVIKTYVELG 237
Cdd:cd08418   80 ARKDHPLQGAR--SLEELLdaswVLP--GTRMG-YYNNLLE-ALRRLGYNPRVAVRTDSIVSIINLVEKA 143
 
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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