NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1881479429|gb|QMF97416|]
View 

LysR family transcriptional regulator [Klebsiella oxytoca]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-268 2.48e-44

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 2.48e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   5 LDVLVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  85 VRLHQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELD--LAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 165 GELTQVFVVSPQHPLAqiteplswrtlrRYRAIANcgllpqaenqdsltvfDLSGQLTLLCAGLGWGYLPLFQVQPLLAR 244
Cdd:COG0583   161 GEERLVLVASPDHPLA------------RRAPLVN----------------SLEALLAAVAAGLGIALLPRFLAADELAA 212

                         250       260
                  ....*....|....*....|....
gi 1881479429 245 GELRIIQTRMVAPVNRAWIGWHEE 268
Cdd:COG0583   213 GRLVALPLPDPPPPRPLYLVWRRR 236
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-268 2.48e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 2.48e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   5 LDVLVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  85 VRLHQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELD--LAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 165 GELTQVFVVSPQHPLAqiteplswrtlrRYRAIANcgllpqaenqdsltvfDLSGQLTLLCAGLGWGYLPLFQVQPLLAR 244
Cdd:COG0583   161 GEERLVLVASPDHPLA------------RRAPLVN----------------SLEALLAAVAAGLGIALLPRFLAADELAA 212

                         250       260
                  ....*....|....*....|....
gi 1881479429 245 GELRIIQTRMVAPVNRAWIGWHEE 268
Cdd:COG0583   213 GRLVALPLPDPPPPRPLYLVWRRR 236
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-247 7.47e-39

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 138.15  E-value: 7.47e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   8 LVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQAVRL 87
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  88 HQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPALSGYGCLLLGEL 167
Cdd:PRK11074   87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 168 TQVFVVSPQHPLAQITEPLSWRTLRRYRAIanC-------------GLLPqaeNQDSLTVFDLSGQLTLLCAGLGWGYLP 234
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSL--CledtsrtlpkritWLLD---NQRRLVVPDWESAINCLSAGLCVGMVP 241

                         250
                  ....*....|...
gi 1881479429 235 LFQVQPLLARGEL 247
Cdd:PRK11074  242 THFAKPLINSGKL 254
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 99-277 1.07e-37

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 132.01  E-value: 1.07e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  99 VDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPAlSGYGCLLLGELTQVFVVSPQHP 178
Cdd:cd08431     6 IDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAVAPNHP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 179 LAQITEPLSWRTLRRYRAIA-----------NCGLLpqaENQDSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPLLARGEL 247
Cdd:cd08431    85 LAKLDGPLDASAIKQYPAIVvadtsrnlpprSSGLL---EGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGEL 161

                         170       180       190
                  ....*....|....*....|....*....|
gi 1881479429 248 RIIQTRMVAPVNRAWIGWHEEGGGLAGEWW 277
Cdd:cd08431   162 VEKALEDPRPPQELFLAWRKDQRGKALAWF 191
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-268 1.01e-17

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: 79.64  E-value: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  94 RLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLLGELTQVFVV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELD--LAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 174 SPQHPLAQiTEPLSWRTLRRYRAI---ANCGLLPQAEN---------QDSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPL 241
Cdd:pfam03466  81 PPDHPLAR-GEPVSLEDLADEPLIllpPGSGLRDLLDRalraaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180
                  ....*....|....*....|....*..
gi 1881479429 242 LARGELRIIQTRMVAPVNRAWIGWHEE 268
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKG 186
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 8-274 2.03e-10

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 60.31  E-value: 2.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   8 LVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRsGHRARFTRTGQMLLEKGRDVlhtaRELEKQAVRL 87
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQV----RLLEAELLAE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  88 HQGWED------RLVLNVDSgfpfhlLA----PLITAFYRQHHATrLEFRRDTLAAGWQTLAEGRAdlLLGVQSDPPALS 157
Cdd:TIGR03298  81 LPGLAPgaptrlTIAVNADS------LAtwflPALAPVLAREGVL-LDLVVEDQDHTAELLRSGEV--LGAVTTEAKPVP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 158 GYGCLLLGELTQVFVVSPQHPLAQITEPLSWRTLRRYRAIA--------------NCGL--------LPQAEnqdsltvf 215
Cdd:TIGR03298 152 GCRVVPLGAMRYLAVASPAFAARYFPDGVTAAALARAPVIVfnrkddlqdrflrrLFGLpvspprhyVPSSE-------- 223

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1881479429 216 dlsGQLTLLCAGLGWGYLPLFQVQPLLARGELRIIQTRMVAPVNRAWIGWHEEGGGLAG 274
Cdd:TIGR03298 224 ---GFVDAARAGLGWGMVPELQAEPHLAAGRLVELAPGRALDVPLYWHHWRLESRLLER 279
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-80 9.47e-09

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.51  E-value: 9.47e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1881479429  17 EGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTAREL 80
Cdd:NF041036   15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSL 78
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-268 2.48e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 2.48e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   5 LDVLVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  85 VRLHQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELD--LAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 165 GELTQVFVVSPQHPLAqiteplswrtlrRYRAIANcgllpqaenqdsltvfDLSGQLTLLCAGLGWGYLPLFQVQPLLAR 244
Cdd:COG0583   161 GEERLVLVASPDHPLA------------RRAPLVN----------------SLEALLAAVAAGLGIALLPRFLAADELAA 212

                         250       260
                  ....*....|....*....|....
gi 1881479429 245 GELRIIQTRMVAPVNRAWIGWHEE 268
Cdd:COG0583   213 GRLVALPLPDPPPPRPLYLVWRRR 236
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-247 7.47e-39

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 138.15  E-value: 7.47e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   8 LVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQAVRL 87
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  88 HQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPALSGYGCLLLGEL 167
Cdd:PRK11074   87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 168 TQVFVVSPQHPLAQITEPLSWRTLRRYRAIanC-------------GLLPqaeNQDSLTVFDLSGQLTLLCAGLGWGYLP 234
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSL--CledtsrtlpkritWLLD---NQRRLVVPDWESAINCLSAGLCVGMVP 241

                         250
                  ....*....|...
gi 1881479429 235 LFQVQPLLARGEL 247
Cdd:PRK11074  242 THFAKPLINSGKL 254
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 99-277 1.07e-37

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 132.01  E-value: 1.07e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  99 VDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPAlSGYGCLLLGELTQVFVVSPQHP 178
Cdd:cd08431     6 IDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAVAPNHP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 179 LAQITEPLSWRTLRRYRAIA-----------NCGLLpqaENQDSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPLLARGEL 247
Cdd:cd08431    85 LAKLDGPLDASAIKQYPAIVvadtsrnlpprSSGLL---EGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGEL 161

                         170       180       190
                  ....*....|....*....|....*....|
gi 1881479429 248 RIIQTRMVAPVNRAWIGWHEEGGGLAGEWW 277
Cdd:cd08431   162 VEKALEDPRPPQELFLAWRKDQRGKALAWF 191
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-275 2.85e-35

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 129.16  E-value: 2.85e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  18 GSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQAVRLHQGWEDR--L 95
Cdd:PRK10094   17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQvnI 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  96 VLNvDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPALSGYGCLLLGELTQVFVVSP 175
Cdd:PRK10094   97 VIN-NLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAA 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 176 QHPLAQITEPLSWRTLRRYRAI-----------ANCGLLPqaeNQDSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPLLAR 244
Cdd:PRK10094  176 DHPLANVEEPLTEAQLRRFPAVniedsartltkRVAWRLP---GQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDN 252

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1881479429 245 GELRIIQTRMVAPVNRAWIGWHEEGGGLAGE 275
Cdd:PRK10094  253 QQLVSRVIPTMRPPSPLSLAWRKFGSGKAVE 283
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-268 1.01e-17

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: 79.64  E-value: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  94 RLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLLGELTQVFVV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELD--LAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 174 SPQHPLAQiTEPLSWRTLRRYRAI---ANCGLLPQAEN---------QDSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPL 241
Cdd:pfam03466  81 PPDHPLAR-GEPVSLEDLADEPLIllpPGSGLRDLLDRalraaglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180
                  ....*....|....*....|....*..
gi 1881479429 242 LARGELRIIQTRMVAPVNRAWIGWHEE 268
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKG 186
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-74 4.99e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.82  E-value: 4.99e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   5 LDVLVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVL 74
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.93e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 63.94  E-value: 1.93e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   5 LDVLVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-191 3.68e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 68.44  E-value: 3.68e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  13 ALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHtarELE--KQAVR---- 86
Cdd:PRK11242   11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ---DLEagRRAIHdvad 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  87 LHQGwedRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLLGE 166
Cdd:PRK11242   88 LSRG---SLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELD--VGIAFAPVHSPEIEAQPLFT 162

                         170       180
                  ....*....|....*....|....*
gi 1881479429 167 LTQVFVVSPQHPLAQITEPLSWRTL 191
Cdd:PRK11242  163 ETLALVVGRHHPLAARRKALTLDEL 187
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-194 8.86e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 67.35  E-value: 8.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   8 LVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVL-HTARELekQAVR 86
Cdd:PRK15421    7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLpQISQAL--QACN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  87 LHQgwEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLgvQSDPPALSGYGCLLLGE 166
Cdd:PRK15421   85 EPQ--QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM--TSDILPRSGLHYSPMFD 160

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1881479429 167 LTQVFVVSPQHPLA---QIT-EPLSWRTLRRY 194
Cdd:PRK15421  161 YEVRLVLAPDHPLAaktRITpEDLASETLLIY 192
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 106-268 7.44e-11

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: 60.31  E-value: 7.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 106 HLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLLGELTQVFVVSPQHPLAQiTEP 185
Cdd:cd05466    13 YLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELD--LAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAK-RKS 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 186 LSWRTLRRYRAI----------------ANCGLLPQAenqdSLTVFDLSGQLTLLCAGLGWGYLPLFQVQpLLARGELRI 249
Cdd:cd05466    90 VTLADLADEPLIlfergsglrrlldrafAEAGFTPNI----ALEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVV 164

                         170
                  ....*....|....*....
gi 1881479429 250 IQTRMVAPVNRAWIGWHEE 268
Cdd:cd05466   165 LPLEDPPLSRTIGLVWRKG 183
PRK09801 PRK09801
LysR family transcriptional regulator;
3-247 1.29e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.20  E-value: 1.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   3 PLLDVLVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEK 82
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  83 QAVRLHQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRrdtLAAGWQTLAEGRADLLLGVQSDPPALsgYGCL 162
Cdd:PRK09801   86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFE---LFDRQIDLVQDNIDLDIRINDEIPDY--YIAH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 163 LLGELTQVFVVSPQHpLAQITEPLSWRTLRRYRAIA------NCGLLPQAENQDSLTV------FDLSGQLTLLCAGLGW 230
Cdd:PRK09801  161 LLTKNKRILCAAPEY-LQKYPQPQSLQELSRHDCLVtkerdmTHGIWELGNGQEKKSVkvsghlSSNSGEIVLQWALEGK 239

                         250
                  ....*....|....*....
gi 1881479429 231 GYL--PLFQVQPLLARGEL 247
Cdd:PRK09801  240 GIMlrSEWDVLPFLESGKL 258
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 8-274 2.03e-10

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 60.31  E-value: 2.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   8 LVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRsGHRARFTRTGQMLLEKGRDVlhtaRELEKQAVRL 87
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQV----RLLEAELLAE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  88 HQGWED------RLVLNVDSgfpfhlLA----PLITAFYRQHHATrLEFRRDTLAAGWQTLAEGRAdlLLGVQSDPPALS 157
Cdd:TIGR03298  81 LPGLAPgaptrlTIAVNADS------LAtwflPALAPVLAREGVL-LDLVVEDQDHTAELLRSGEV--LGAVTTEAKPVP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 158 GYGCLLLGELTQVFVVSPQHPLAQITEPLSWRTLRRYRAIA--------------NCGL--------LPQAEnqdsltvf 215
Cdd:TIGR03298 152 GCRVVPLGAMRYLAVASPAFAARYFPDGVTAAALARAPVIVfnrkddlqdrflrrLFGLpvspprhyVPSSE-------- 223

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1881479429 216 dlsGQLTLLCAGLGWGYLPLFQVQPLLARGELRIIQTRMVAPVNRAWIGWHEEGGGLAG 274
Cdd:TIGR03298 224 ---GFVDAARAGLGWGMVPELQAEPHLAAGRLVELAPGRALDVPLYWHHWRLESRLLER 279
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-250 1.70e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 57.48  E-value: 1.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  11 LDALD---KEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRsGHRARFTRTGQMLLEKGR-------DVLHTAREL 80
Cdd:PRK03635    7 LEALAavvREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARqvrlleaELLGELPAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  81 EKQAVRLhqgwedRLVLNVDSgfpfhlLA----PLITAFYRQHHAtRLEFRRDTLAAGWQTLAEGRAdllLG-VQSDPPA 155
Cdd:PRK03635   86 DGTPLTL------SIAVNADS------LAtwflPALAPVLARSGV-LLDLVVEDQDHTAELLRRGEV---VGaVTTEPQP 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 156 LSGYGCLLLGELTQVFVVSP------------QHPLAQIteP---------LSWRTLRRYRAIA----NCGLLPQAEnqd 210
Cdd:PRK03635  150 VQGCRVDPLGAMRYLAVASPafaaryfpdgvtAEALAKA--PavvfnrkddLQDRFLRQAFGLPpgsvPCHYVPSSE--- 224

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1881479429 211 sltvfdlsGQLTLLCAGLGWGYLPLFQVQPLLARGELRII 250
Cdd:PRK03635  225 --------AFVRAALAGLGWGMIPELQIEPELASGELVDL 256
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-80 9.47e-09

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.51  E-value: 9.47e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1881479429  17 EGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTAREL 80
Cdd:NF041036   15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSL 78
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-250 2.94e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 54.00  E-value: 2.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  18 GSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQAVRLHQGWEDRLVL 97
Cdd:PRK10632   17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRI 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  98 NVDSGFPFHLLAPLITAFYRQHHATRLefrrdTLAAGWQT---LAEGradLLLGVQSDPPALSGYGCLLLGELTQVfVVS 174
Cdd:PRK10632   97 GCSSTMAQNVLAGLTAKMLKEYPGLSV-----NLVTGIPApdlIADG---LDVVIRVGALQDSSLFSRRLGAMPMV-VCA 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 175 PQHPLAQITEP--------LSW-----RTLRRYRAIANCGLLPQAENQDSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPL 241
Cdd:PRK10632  168 AKSYLAQYGTPekpadlssHSWleysvRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPLMWVIDE 247


                  ....*....
gi 1881479429 242 LARGELRII 250
Cdd:PRK10632  248 INRGELEIL 256
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-268 6.85e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.67  E-value: 6.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  11 LDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHrARFTRTGQMLLEKGR-------DVLHTARELEKQ 83
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRqvalleaDLLSTLPAERGS 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  84 AVRLhqgwedRLVLNVDSgfpfhlLA----PLITAFYRQHHaTRLEFRRD----TLAAgwqtLAEGRAdllLG-VQSDPP 154
Cdd:PRK13348   89 PPTL------AIAVNADS------LAtwflPALAAVLAGER-ILLELIVDdqdhTFAL----LERGEV---VGcVSTQPK 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 155 ALSGYGCLLLGELTQVFVVSPQHPLAQITEPLSWRTLRRYRAIAncgllpqAENQDSL------TVFDLS---------- 218
Cdd:PRK13348  149 PMRGCLAEPLGTMRYRCVASPAFAARYFAQGLTRHSALKAPAVA-------FNRKDTLqdsfleQLFGLPvgayprhyvp 221

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1881479429 219 ---GQLTLLCAGLGWGYLPLFQVQPLLARGELRIIQTRMVAPVNRAWIGWHEE 268
Cdd:PRK13348  222 sthAHLAAIRHGLGYGMVPELLIGPLLAAGRLVDLAPGHPVDVALYWHHWEVE 274
PRK09986 PRK09986
LysR family transcriptional regulator;
13-181 8.13e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 52.42  E-value: 8.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  13 ALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQAVRLHQGWE 92
Cdd:PRK09986   17 AVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  93 DRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRdtLAAGWQTLAEGRADLLLGVQ--SDPPALSGYGCLLLGELTQV 170
Cdd:PRK09986   97 GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRE--LSPSMQMAALERRELDAGIWrmADLEPNPGFTSRRLHESAFA 174

                         170
                  ....*....|.
gi 1881479429 171 FVVSPQHPLAQ 181
Cdd:PRK09986  175 VAVPEEHPLAS 185
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-181 1.18e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.92  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  16 KEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEkqavRLHQGWEDRL 95
Cdd:PRK10837   16 KSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE----QLFREDNGAL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  96 VLNVDSGFPFHLLAPLITAFYRQHHATRLEFR----RDTLAAgwqtLAEGRADLLL--GVQSDPPALSgyGCLLLGELtq 169
Cdd:PRK10837   92 RIYASSTIGNYILPAMIARYRRDYPQLPLELSvgnsQDVINA----VLDFRVDIGLieGPCHSPELIS--EPWLEDEL-- 163

                         170
                  ....*....|..
gi 1881479429 170 VFVVSPQHPLAQ 181
Cdd:PRK10837  164 VVFAAPDSPLAR 175
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-181 1.42e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 48.61  E-value: 1.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  13 ALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTArelEKQAVRLHQGWE 92
Cdd:PRK09906   11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQA---EKAKLRARKIVQ 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  93 DRLVLNVdsGF----PFHLLAPLITAFYRQHHATRLEFRrdTLAAGWQTLAEGRADLLLGVQSDPPALSGYGCLLLGELT 168
Cdd:PRK09906   88 EDRQLTI--GFvpsaEVNLLPKVLPMFRLRHPDTLIELV--SLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEP 163

                         170
                  ....*....|...
gi 1881479429 169 QVFVVSPQHPLAQ 181
Cdd:PRK09906  164 LVVVLPVDHPLAH 176
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-250 1.58e-06

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: 47.82  E-value: 1.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  94 RLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFrrdtlaagwqTLAEGRADLL-----LGVQSDPPALSGYGCLLLGELT 168
Cdd:cd08422     2 RLRISAPVSFGRLHLAPLLAEFLARYPDVRLEL----------VLSDRLVDLVeegfdLAIRIGELPDSSLVARRLGPVR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 169 QVFVVSPQHpLAQITEPLSWRTLRRYRAIANCGLLPQA----ENQDSLTVFDLSGQLT---------LLCAGLGWGYLPL 235
Cdd:cd08422    72 RVLVASPAY-LARHGTPQTPEDLARHRCLGYRLPGRPLrwrfRRGGGEVEVRVRGRLVvndgealraAALAGLGIALLPD 150

                         170
                  ....*....|....*
gi 1881479429 236 FQVQPLLARGELRII 250
Cdd:cd08422   151 FLVAEDLASGRLVRV 165
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 23-264 2.21e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 48.12  E-value: 2.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  23 ASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHR-ARFTRTGQMLLEKGRDVLHTARELEKQAVRLHQGWEDRLVLNVDS 101
Cdd:PRK12683   22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRlTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTH 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 102 GFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLllGVQSDppALSGYGCLLLGELTQ---VFVVSPQHP 178
Cdd:PRK12683  102 TQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADI--GIATE--ALDREPDLVSFPYYSwhhVVVVPKGHP 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 179 LAQItEPLSWRTLRRY----------------RAIANCGLLPQAenqdSLTVFDLSGQLTLLCAGLGWGYLPLFQVQPLL 242
Cdd:PRK12683  178 LTGR-ENLTLEAIAEYpiitydqgftgrsridQAFAEAGLVPDI----VLTALDADVIKTYVELGMGVGIVAAMAYDPQR 252

                         250       260
                  ....*....|....*....|..
gi 1881479429 243 ARGeLRIIQTRMVAPVNRAWIG 264
Cdd:PRK12683  253 DTG-LVALDTDHLFEANTTRVG 273
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-119 4.13e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 47.53  E-value: 4.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  19 SFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLH-----TARELEKQAVRlhqgwed 93
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDqlaeaTRKLRARSAKG------- 94

                          90       100
                  ....*....|....*....|....*.
gi 1881479429  94 RLVLNVDSGFPFHLLAPLITAFYRQH 119
Cdd:PRK11139   95 ALTVSLLPSFAIQWLVPRLSSFNEAH 120
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 106-273 6.90e-06

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: 45.73  E-value: 6.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 106 HLLAPLITAFYRQHHATRLEFRRDT---LAAGwqtLAEGRADLLLGVQSDPPALSGYGCLLLGELTQVFVVSPQHPLAQi 182
Cdd:cd08435    13 VLLPPAIARLLARHPRLTVRVVEGTsdeLLEG---LRAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGHPLAR- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 183 TEPLSWRTLRRYR-AIANCGLLPQAENQDSLTVfdlsgqltllcAGLGwgyLPLFQVQ---PLLARGELriIQTRMVAPV 258
Cdd:cd08435    89 RARLTLADLADYPwVLPPPGTPLRQRLEQLFAA-----------AGLP---LPRNVVEtasISALLALL--ARSDMLAVL 152

                         170
                  ....*....|....*
gi 1881479429 259 NRAWIGWHEEGGGLA 273
Cdd:cd08435   153 PRSVAEDELRAGVLR 167
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-127 9.97e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 46.15  E-value: 9.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  19 SFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQML---LEKGRDVLhtARELEKQAvrlHQGWEDRL 95
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSSLDTL--NQEILDIK---NQELSGTL 104

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1881479429  96 VLNVDSGFPFHLLAPLITAFYRQHHATRLEFR 127
Cdd:PRK10086  105 TVYSRPSIAQCWLVPRLADFTRRYPSISLTIL 136
PRK10341 PRK10341
transcriptional regulator TdcA;
8-174 7.80e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 43.70  E-value: 7.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   8 LVILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKgrdVLHTARELeKQAVRL 87
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR---SESITREM-KNMVNE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  88 HQGWEDRLVLNVDSGFP----FHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPALSGYGCLL 163
Cdd:PRK10341   88 INGMSSEAVVDVSFGFPsligFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHVEP 167

                         170
                  ....*....|.
gi 1881479429 164 LGELTQVFVVS 174
Cdd:PRK10341  168 LFESEFVLVAS 178
PRK12680 PRK12680
LysR family transcriptional regulator;
15-233 1.88e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 42.30  E-value: 1.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  15 DKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRAR-FTRTGQMLLEKGRDVLHTARELEKQAV---RLHQG 90
Cdd:PRK12680   14 DAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAAnqrRESQG 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  91 wedRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLgVQSDPPALSGYGCLLLGELTQV 170
Cdd:PRK12680   94 ---QLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAI-VSTAGGEPSAGIAVPLYRWRRL 169

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1881479429 171 FVVSPQHPLAQITEPLSWRTLRRY----------------RAIANCGLLPQAenqdSLTVFDLSGQLTLLCAGLGWGYL 233
Cdd:PRK12680  170 VVVPRGHALDTPRRAPDMAALAEHplisyesstrpgsslqRAFAQLGLEPSI----ALTALDADLIKTYVRAGLGVGLL 244
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 21-264 2.23e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 2.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  21 AAASAkLYKTPSALSYTIHKLESDLNIQLLDRSGHR-ARFTRTGQMLLEKGRDVLHTARELEKQAvrlhqgwedRLVLNV 99
Cdd:PRK12682   21 EAAKA-LHTSQPGVSKAIIELEEELGIEIFIRHGKRlKGLTEPGKAVLDVIERILREVGNIKRIG---------DDFSNQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 100 DSG----FPFH-----LLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQS--DPPALSGYGCLllgELT 168
Cdd:PRK12682   91 DSGtltiATTHtqaryVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESlaDDPDLATLPCY---DWQ 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 169 QVFVVSPQHPLAQiTEPLSWRTLRRY----------------RAIANCGLLPQAenqdSLTVFDLSGQLTLLCAGLGWGY 232
Cdd:PRK12682  168 HAVIVPPDHPLAQ-EERITLEDLAEYplityhpgftgrsridRAFAAAGLQPDI----VLEAIDSDVIKTYVRLGLGVGI 242

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1881479429 233 LPLFQVQPlLARGELRIIQTRMVAPVNRAWIG 264
Cdd:PRK12682  243 VAEMAYRP-DRDGDLVALPAGHLFGPNTAWVA 273
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 107-195 3.13e-04

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: 41.05  E-value: 3.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 107 LLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQSDPPAlsGYGCLLLGELTQVFVVSPQHPLAQitEPL 186
Cdd:cd08417    14 LLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPP--GLRSQPLFEDRFVCVARKDHPLAG--GPL 89


                  ....*....
gi 1881479429 187 SWRTLRRYR 195
Cdd:cd08417    90 TLEDYLAAP 98
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 34-84 3.87e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 41.17  E-value: 3.87e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1881479429  34 LSYTIHKLESDLNIQLLDRSGHRARFTRTGQMLLEKGRDVLHTARELEKQA 84
Cdd:PRK11151   32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-262 5.04e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 40.23  E-value: 5.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 106 HLLAPLITAFYRQHHATRLEFrrdtlaagwqTLAEGRADLL-----LGVQS-DPPALSGYGCLLLGELTQVFVVSPQHpL 179
Cdd:cd08475    14 LCVAPLLLELARRHPELELEL----------SFSDRFVDLIeegidLAVRIgELADSTGLVARRLGTQRMVLCASPAY-L 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 180 AQITEPLSWRTLRRYRAIA-NCGLLPQ----AENQDSLTVF---------DLSGQLTLLCAGLGWGYLPLFQVQPLLARG 245
Cdd:cd08475    83 ARHGTPRTLEDLAEHQCIAyGRGGQPLpwrlADEQGRLVRFrpaprlqfdDGEAIADAALAGLGIAQLPTWLVADHLQRG 162

                         170       180
                  ....*....|....*....|
gi 1881479429 246 ELRII---QTRMVAPVNRAW 262
Cdd:cd08475   163 ELVEVlpeLAPEGLPIHAVW 182
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-264 1.63e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 39.41  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429   9 VILDALDKEGSFAAASAKLYKTPSALSYTIHKLESDLNIQLLDRSGHRAR-FTRTGQMLLEKGRDVLHTARELEKQAVRL 87
Cdd:PRK12679    8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  88 HQGWEDRLVLNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLLGVQ--SDPPALSGYGCLllg 165
Cdd:PRK12679   88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASErlSNDPQLVAFPWF--- 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 166 ELTQVFVVSPQHPLAQITePLSWRTLRRY----------------RAIANCGLLPQA--ENQDSLTVfdlsgqLTLLCAG 227
Cdd:PRK12679  165 RWHHSLLVPHDHPLTQIT-PLTLESIAKWplityrqgitgrsridDAFARKGLLADIvlSAQDSDVI------KTYVALG 237

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1881479429 228 LGWGYLPLfQVQPLLARGELRIIQTRMVAPVNRAWIG 264
Cdd:PRK12679  238 LGIGLVAE-QSSGEQEESNLIRLDTRHLFDANTVWLG 273
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-199 2.85e-03

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: 37.89  E-value: 2.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 105 FHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLLGELTQVFVVSPQHPLAQItE 184
Cdd:cd08440    12 ATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVD--FGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARR-R 88

                          90
                  ....*....|....*
gi 1881479429 185 PLSWRTLRRYRAIAN 199
Cdd:cd08440    89 SVTWAELAGYPLIAL 103
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 107-249 3.88e-03

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 37.57  E-value: 3.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 107 LLAPLITAFYRQHHATRLEFRRD---TLAAgWqtLAEGRADLllGVQSDPPALSGYGCLLLGElTQVFVVSPQHPLAQIT 183
Cdd:cd08433    14 LAVPLLRAVRRRYPGIRLRIVEGlsgHLLE-W--LLNGRLDL--ALLYGPPPIPGLSTEPLLE-EDLFLVGPADAPLPRG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 184 EPLSWRTLRRYR------------------AIANCGLLPQAEnQDSLTVfdlsgQLTLLCAGLGWGYLPLFQVQPLLARG 245
Cdd:cd08433    88 APVPLAELARLPlilpsrghglrrlvdeaaARAGLTLNVVVE-IDSVAT-----LKALVAAGLGYTILPASAVAAEVAAG 161


                  ....
gi 1881479429 246 ELRI 249
Cdd:cd08433   162 RLVA 165
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-247 4.56e-03

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 37.67  E-value: 4.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 102 GFPFHLLAPLITAFYRQHhaTRLEFR------RDTLAAgwqtLAEGRADLllGVQSDPPALSGYGCLLLGELTQVFVVSP 175
Cdd:cd08426     9 GLAAELLPSLIARFRQRY--PGVFFTvdvastADVLEA----VLSGEADI--GLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429 176 QHPLAQITEPlSWRTLRRYRAIANC------GLLPQAENQDSLTV--------FDLSGQLTLlcAGLGWGYLPLFQVQPL 241
Cdd:cd08426    81 GHPLARQPSV-TLAQLAGYPLALPPpsfslrQILDAAFARAGVQLepvlisnsIETLKQLVA--AGGGISLLTELAVRRE 157


                  ....*.
gi 1881479429 242 LARGEL 247
Cdd:cd08426   158 IRRGQL 163
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 107-181 6.28e-03

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: 37.16  E-value: 6.28e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1881479429 107 LLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADllLGVQSDPPALSGYGCLLLGELTQVFVVSPQHPLAQ 181
Cdd:cd08415    14 LLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQAD--LGLASLPLDHPGLESEPLASGRAVCVLPPGHPLAR 86
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-197 7.70e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 37.26  E-value: 7.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  21 AAASAkLYKTPSALSYTIHKLESDLNIQLLDRSGHRAR-FTRTGQMLLEKGRDVLHTARELE---KQAVRLHQGwedRLV 96
Cdd:PRK12684   21 EAAKA-LYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKrvgKEFAAQDQG---NLT 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  97 LNVDSGFPFHLLAPLITAFYRQHHATRLEFRRDTLAAGWQTLAEGRADLLL---GVQSDPP--ALSGYgclllgELTQVF 171
Cdd:PRK12684   97 IATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIateAIADYKElvSLPCY------QWNHCV 170

                         170       180
                  ....*....|....*....|....*.
gi 1881479429 172 VVSPQHPLAQiTEPLSWRTLRRYRAI 197
Cdd:PRK12684  171 VVPPDHPLLE-RKPLTLEDLAQYPLI 195
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 98-181 8.69e-03

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: 36.75  E-value: 8.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1881479429  98 NVDSGFPF----HLLAPLITAFYRQHHATRLEFR---RDTLAAGwqtLAEGRADLllGVQSDPPALSGYGCLLLGELTQV 170
Cdd:cd08434     1 TVRLGFLHslgtSLVPDLIRAFRKEYPNVTFELHqgsTDELLDD---LKNGELDL--ALCSPVPDEPDIEWIPLFTEELV 75

                          90
                  ....*....|.
gi 1881479429 171 FVVSPQHPLAQ 181
Cdd:cd08434    76 LVVPKDHPLAG 86
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH