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Conserved domains on  [gi|1236167521|ref|WP_094960519|]
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MULTISPECIES: LysR family transcriptional regulator [Providencia]

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 super family cl43195
DNA-binding transcriptional regulator, LysR family [Transcription];
5-72 1.83e-16

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


The actual alignment was detected with superfamily member COG0583:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 77.21  E-value: 1.83e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDL 72
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRI 71
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-72 1.83e-16

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 77.21  E-value: 1.83e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDL 72
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRI 71
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-63 6.70e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.49  E-value: 6.70e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQ 63
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-77 3.19e-10

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: 59.55  E-value: 3.19e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRD-LYLQEK 77
Cdd:NF040786    4 KQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEmLDLWEK 77
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-78 7.32e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.44  E-value: 7.32e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   1 MFFSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKfGMTLTKDGQELYNDLRDLYLQEKE 78
Cdd:PRK13348    1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLLRHLRQVALLEAD 77
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-72 1.83e-16

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 77.21  E-value: 1.83e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDL 72
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRI 71
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-63 6.70e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.49  E-value: 6.70e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQ 63
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-77 3.19e-10

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: 59.55  E-value: 3.19e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRD-LYLQEK 77
Cdd:NF040786    4 KQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEmLDLWEK 77
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-78 7.32e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.44  E-value: 7.32e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   1 MFFSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKfGMTLTKDGQELYNDLRDLYLQEKE 78
Cdd:PRK13348    1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLLRHLRQVALLEAD 77
PRK09791 PRK09791
LysR family transcriptional regulator;
6-66 1.90e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.46  E-value: 1.90e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1236167521   6 KLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELY 66
Cdd:PRK09791    9 QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFY 69
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-71 4.35e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 53.27  E-value: 4.35e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1236167521   1 MFFSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRD 71
Cdd:PRK10094    1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARD 71
PRK09986 PRK09986
LysR family transcriptional regulator;
5-72 9.82e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 49.34  E-value: 9.82e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDL 72
Cdd:PRK09986   10 KLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRL 77
PRK10341 PRK10341
transcriptional regulator TdcA;
4-67 2.16e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 48.32  E-value: 2.16e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1236167521   4 SRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYN 67
Cdd:PRK10341    9 TQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS 72
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
2-74 1.00e-05

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 46.20  E-value: 1.00e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1236167521   2 FFSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDLYL 74
Cdd:PRK15243    4 LINKKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYI 76
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 5-82 1.99e-05

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 45.15  E-value: 1.99e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRdLYLQEKEITKK 82
Cdd:PRK09906    4 RHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAR-AILEQAEKAKL 80
PRK09801 PRK09801
LysR family transcriptional regulator;
3-66 4.76e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 44.26  E-value: 4.76e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1236167521   3 FSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELY 66
Cdd:PRK09801    7 LAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY 70
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-53 8.23e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 43.44  E-value: 8.23e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREK 53
Cdd:PRK11013    7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVR 55
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 7-82 8.82e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 43.29  E-value: 8.82e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1236167521   7 LEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDLYLQEKEITKK 82
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRK 86
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-66 5.63e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 40.82  E-value: 5.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELY 66
Cdd:PRK11233    4 RRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILY 65
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-79 8.38e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 40.06  E-value: 8.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1236167521   5 RKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELYNDLRDLYLQEKEI 79
Cdd:PRK10837    6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-66 1.46e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 39.59  E-value: 1.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1236167521  10 FMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELY 66
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFY 66
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-66 1.61e-03

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 39.60  E-value: 1.61e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1236167521   6 KLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQELY 66
Cdd:PRK10086   18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF 78
rbcR CHL00180
LysR transcriptional regulator; Provisional
 2-65 3.02e-03

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 38.46  E-value: 3.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1236167521   2 FFSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKFGMTLTKDGQEL 65
Cdd:CHL00180    5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELL 68
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-78 5.71e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 37.83  E-value: 5.71e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1236167521   1 MFFSRKLEAFMAVVENGSLSKAARVMNRTTPPIAKSIKDFETSLGKRLFKREKfGMTLTKDGQELYNDLRDLYLQEKE 78
Cdd:PRK03635    1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLLRHARQVRLLEAE 77
 
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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