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Conserved domains on  [gi|491594777|ref|WP_005452341|]
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MULTISPECIES: LysR family transcriptional regulator [Vibrio]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-264 6.44e-36

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 129.22  E-value: 6.44e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYRELITTAIQMNIS 90
Cdd:COG0583    9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  91 EQIVYRVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGnPYHKTNNDFNIDELFHVNCWW 170
Cdd:COG0583   89 PRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR-LGPPPDPGLVARPLGEERLVL 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777 171 VAHED--LASVTSnpsqrvllmdgceellnlsniasynlwRLDDLGTILDLCKAQRGMAFLPEFLIEKNMKENKLKIItD 248
Cdd:COG0583  168 VASPDhpLARRAP---------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVAL-P 219

                        250
                 ....*....|....*.
gi 491594777 249 HPDFFGKRVVaSLFWP 264
Cdd:COG0583  220 LPDPPPPRPL-YLVWR 234
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-264 6.44e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 129.22  E-value: 6.44e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYRELITTAIQMNIS 90
Cdd:COG0583    9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  91 EQIVYRVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGnPYHKTNNDFNIDELFHVNCWW 170
Cdd:COG0583   89 PRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR-LGPPPDPGLVARPLGEERLVL 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777 171 VAHED--LASVTSnpsqrvllmdgceellnlsniasynlwRLDDLGTILDLCKAQRGMAFLPEFLIEKNMKENKLKIItD 248
Cdd:COG0583  168 VASPDhpLARRAP---------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVAL-P 219

                        250
                 ....*....|....*.
gi 491594777 249 HPDFFGKRVVaSLFWP 264
Cdd:COG0583  220 LPDPPPPRPL-YLVWR 234
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 6.72e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.28  E-value: 6.72e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777    5 FENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 11-147 6.39e-18

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 81.89  E-value: 6.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFhlsapvvsRYrelittAIQM-NI 89
Cdd:NF040786   9 FVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLY--------EY------AKEMlDL 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777  90 SEQIVyrvgidpLVFNKDVKKT--------------------LLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLAL 147
Cdd:NF040786  75 WEKLE-------EEFDRYGKESkgvlrigastipgqyllpelLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGF 145
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-147 8.94e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 67.33  E-value: 8.94e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777   4 QFENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHlsapVVSRYRELITT 83
Cdd:PRK10086  15 QLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFW----ALKSSLDTLNQ 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491594777  84 AIQ----MNISEQI-VY-RVGIDP--LVfnkdvkKTLLDFSEAFPNVDLVVVTkpsfilGN-YIN--EGKIDLAL 147
Cdd:PRK10086  91 EILdiknQELSGTLtVYsRPSIAQcwLV------PRLADFTRRYPSISLTILT------GNeNVNfqRAGIDLAI 153
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-235 3.92e-07

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 49.52  E-value: 3.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  96 RVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGNpYHKTNNDFNIDELFHVNCWWVAH-- 173
Cdd:cd05466    3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA-LPVDDPGLESEPLFEEPLVLVVPpd 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777 174 -----------EDLASV-----TSNPSQRVLLMDGCEELLNLSNIASynlwRLDDLGTILDLCKAQRGMAFLPEFLIE 235
Cdd:cd05466   82 hplakrksvtlADLADEplilfERGSGLRRLLDRAFAEAGFTPNIAL----EVDSLEAIKALVAAGLGIALLPESAVE 155
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-264 6.44e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 129.22  E-value: 6.44e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYRELITTAIQMNIS 90
Cdd:COG0583    9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  91 EQIVYRVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGnPYHKTNNDFNIDELFHVNCWW 170
Cdd:COG0583   89 PRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR-LGPPPDPGLVARPLGEERLVL 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777 171 VAHED--LASVTSnpsqrvllmdgceellnlsniasynlwRLDDLGTILDLCKAQRGMAFLPEFLIEKNMKENKLKIItD 248
Cdd:COG0583  168 VASPDhpLARRAP---------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVAL-P 219

                        250
                 ....*....|....*.
gi 491594777 249 HPDFFGKRVVaSLFWP 264
Cdd:COG0583  220 LPDPPPPRPL-YLVWR 234
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 6.72e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.28  E-value: 6.72e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777    5 FENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 11-147 6.39e-18

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 81.89  E-value: 6.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFhlsapvvsRYrelittAIQM-NI 89
Cdd:NF040786   9 FVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLY--------EY------AKEMlDL 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777  90 SEQIVyrvgidpLVFNKDVKKT--------------------LLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLAL 147
Cdd:NF040786  75 WEKLE-------EEFDRYGKESkgvlrigastipgqyllpelLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGF 145
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-147 8.94e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 67.33  E-value: 8.94e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777   4 QFENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHlsapVVSRYRELITT 83
Cdd:PRK10086  15 QLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFW----ALKSSLDTLNQ 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491594777  84 AIQ----MNISEQI-VY-RVGIDP--LVfnkdvkKTLLDFSEAFPNVDLVVVTkpsfilGN-YIN--EGKIDLAL 147
Cdd:PRK10086  91 EILdiknQELSGTLtVYsRPSIAQcwLV------PRLADFTRRYPSISLTILT------GNeNVNfqRAGIDLAI 153
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-126 9.90e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 64.19  E-value: 9.90e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  13 AVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGkRLFhlsapvVSRYRELITtaiQMNISEQ 92
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAG-EWF------VKEARSVIK---KMQETRR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 491594777  93 IVYRVG----------IDPLVFNKDVKKTLLDFSEAFPNVDLVV 126
Cdd:PRK11074  82 QCQQVAngwrgqlsiaVDNIVRPDRTRQLIVDFYRHFDDVELII 125
PRK09801 PRK09801
LysR family transcriptional regulator;
11-98 8.00e-11

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.59  E-value: 8.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYRELITTAIQMNIS 90
Cdd:PRK09801  14 LVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTR 93


                 ....*...
gi 491594777  91 EQIVYRVG 98
Cdd:PRK09801  94 PEGMIRIG 101
PRK10341 PRK10341
transcriptional regulator TdcA;
6-148 4.57e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 59.49  E-value: 4.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777   6 ENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYRELITTAI 85
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491594777  86 QMNISEQIVYRVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALG 148
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIG 152
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-67 5.50e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 59.26  E-value: 5.50e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 491594777  13 AVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLF 67
Cdd:CHL00180  15 AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLL 69
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-235 1.94e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 57.72  E-value: 1.94e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777   3 LQFENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRyrelIT 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ----IS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  83 TAIQM-NISEQIVYRVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGNP-------YHKT 154
Cdd:PRK15421  78 QALQAcNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDilprsglHYSP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777 155 NNDFNI------DELFHVNCwWVAHEDLASVT--SNPSQRVLLmDGCEELLNLSNIaSYNLWRLDDLGTILDLCKAQRGM 226
Cdd:PRK15421 158 MFDYEVrlvlapDHPLAAKT-RITPEDLASETllIYPVQRSRL-DVWRHFLQPAGV-SPSLKSVDNTLLLIQMVAARMGI 234


                 ....*....
gi 491594777 227 AFLPEFLIE 235
Cdd:PRK15421 235 AALPHWVVE 243
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-68 2.97e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.08  E-value: 2.97e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFH 68
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQ 67
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 10-147 8.68e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.42  E-value: 8.68e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  10 SFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYRELITTAIQMNI 89
Cdd:PRK15092  18 TFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYSNL 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491594777  90 seQIVYRVGIdplvfNKDVKKTLLDF-----SEAFPNVDLVVVTKPSFILGNYINEGKIDLAL 147
Cdd:PRK15092  98 --QGVLTIGA-----SDDTADTILPFllnrvSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-66 1.34e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 54.81  E-value: 1.34e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491594777   6 ENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRL 66
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHL 65
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-63 4.92e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 53.23  E-value: 4.92e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKG 63
Cdd:PRK09906   9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAG 61
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-69 1.44e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.90  E-value: 1.44e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSkVWLTEKGKRLF-HL 69
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLrHL 68
PRK09986 PRK09986
LysR family transcriptional regulator;
11-68 1.56e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 51.65  E-value: 1.56e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFH 68
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILME 72
PRK09791 PRK09791
LysR family transcriptional regulator;
3-67 2.80e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.92  E-value: 2.80e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491594777   3 LQFENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLF 67
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFY 69
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-235 3.92e-07

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 49.52  E-value: 3.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  96 RVGIDPLVFNKDVKKTLLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGNpYHKTNNDFNIDELFHVNCWWVAH-- 173
Cdd:cd05466    3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA-LPVDDPGLESEPLFEEPLVLVVPpd 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777 174 -----------EDLASV-----TSNPSQRVLLMDGCEELLNLSNIASynlwRLDDLGTILDLCKAQRGMAFLPEFLIE 235
Cdd:cd05466   82 hplakrksvtlADLADEplilfERGSGLRRLLDRAFAEAGFTPNIAL----EVDSLEAIKALVAAGLGIALLPESAVE 155
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-63 8.22e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 49.57  E-value: 8.22e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491594777   7 NIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKG 63
Cdd:PRK11242   5 HIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAG 61
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
13-66 2.95e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.85  E-value: 2.95e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491594777  13 AVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNsKVWLTEKGKRL 66
Cdd:PRK03635  12 AVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRL 64
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 112-246 4.16e-06

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: 46.51  E-value: 4.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777  112 LLDFSEAFPNVDLVVVTKPSFILGNYINEGKIDLALGNPyHKTNNDFNIDELFHVNCWWVAHED--LASVTS-NPSQ--- 185
Cdd:pfam03466  21 LARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG-PPDDPGLEARPLGEEPLVLVAPPDhpLARGEPvSLEDlad 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491594777  186 --RVLLMDGC------EELLNLSNIASYNLWRLDDLGTILDLCKAQRGMAFLPEFLIEKNMKENKLKII 246
Cdd:pfam03466 100 epLILLPPGSglrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADGRLVAL 168
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 11-67 5.03e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 46.99  E-value: 5.03e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491594777  11 FVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLF 67
Cdd:PRK10837  11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY 67
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-67 9.11e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.52  E-value: 9.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491594777   1 MKLQFENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLF 67
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLF 68
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-67 1.20e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 45.99  E-value: 1.20e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 491594777  19 SFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLF 67
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYF 70
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 2-74 1.30e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 45.75  E-value: 1.30e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491594777   2 KLQFENIVSFVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLF-HLSAPVV 74
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYeHCKAMLV 74
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-80 1.22e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 42.88  E-value: 1.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491594777  30 SQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRLFHLSAPVVSRYREL 80
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL 54
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
19-91 1.69e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 42.35  E-value: 1.69e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491594777  19 SFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKrLFHlsapvvSRYRELITTaIQMNISE 91
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGK-IFH------SQIRHLLQQ-LESNLAE 91
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
20-66 3.76e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 41.16  E-value: 3.76e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 491594777  20 FSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSKVWLTEKGKRL 66
Cdd:PRK03601  18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERL 64
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-66 5.08e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 41.12  E-value: 5.08e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491594777   1 MKLQFENIVsfVAVVEEG-SFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQNSK-VWLTEKGKRL 66
Cdd:PRK12684   1 MNLHQLRFV--REAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRlRGLTEPGRII 66
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-125 6.82e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 40.80  E-value: 6.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777   1 MKLQFENIVSfVAVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRqnskvwlteKGKRLFHLSAPvvsrYREL 80
Cdd:PRK12683   1 MNFQQLRIIR-EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIR---------RGKRLTGLTEP----GKEL 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491594777  81 ITTAIQMNISEQIVYRVGIDplvFNKDVKKTLL-----------------DFSEAFPNVDLV 125
Cdd:PRK12683  67 LQIVERMLLDAENLRRLAEQ---FADRDSGHLTvatthtqaryalpkvvrQFKEVFPKVHLA 125
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-92 2.58e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.82  E-value: 2.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491594777   1 MKL-QFEnivsFV--AVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQnskvwltekGKRLFHLSAP--VVS 75
Cdd:PRK12682   1 MNLqQLR----FVreAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRH---------GKRLKGLTEPgkAVL 67

                         90
                 ....*....|....*....
gi 491594777  76 RYRELITTAIQ--MNISEQ 92
Cdd:PRK12682  68 DVIERILREVGniKRIGDD 86
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
13-80 3.56e-03

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 36.72  E-value: 3.56e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491594777  13 AVVEEGSFSSAARKLGKSQSTVSTAVQNLESDLGFNLFNRQ-------NSKvwLTEKGKRLfhlsapvVSRYREL 80
Cdd:COG2005   29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQtggkgggGAR--LTPEGRRL-------LALYRRL 94
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
24-96 9.32e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 35.56  E-value: 9.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491594777  24 ARKLGKSQSTVSTAVQNLESDlGFnLFNRQNSKVWLTEKGKRlfhLSAPVVSRYReLITT--AIQMNISEQIVYR 96
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLEEK-GL-VEYEPYGGITLTEEGRE---LALRIVRRHR-LLERflVEVLGVDWDEAHE 99
 
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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