NCBI Conserved Domain Search

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Conserved domains on [gi\|119717534\|ref\|YP_924499.1\|]
regulatory protein, LuxR [Nocardioides sp. JS614]

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List of domain hits		?

References:

Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.

Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.

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of the residues that compose this conserved feature have been mapped to the query sequence.

Click on the triangle to view details about the feature, including a multiple sequence alignment of your query sequence and the protein sequences used to curate the domain model, where hash marks (#) above the aligned sequences show the location of the conserved feature residues.

The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions. Click on the triangle for interactive 3D structure viewing options.

This image shows a graphical summary of conserved domains identified on the query sequence. The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits (labeled illustration) or all hits (labeled illustration).
Domains are color coded according to superfamilies to which they have been assigned. Hits with scores that pass a domain-specific threshold (specific hits) are drawn in bright colors. Others (non-specific hits) and superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features), they are mapped to the query sequence and indicated through sets of triangles with the same color and shade of the domain or superfamily that provides the annotation.
Mouse over the colored bars or triangles to see descriptions of the domains and features. click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.

The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores. Click on the PssmId to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.

To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page, or click on the triangles, if present, that represent functional sites (conserved features) mapped to the query sequence.

Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence. (labeled illustration)
Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance. (labeled illustration)
Four types of hits can be shown, as available, for each region on the query sequence:

specific hits meet or exceed a domain-specific e-value threshold (illustrated example) and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains

The CD-Search help document provides more detail about the tool and its features.

Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool (CDART).

Modify your query to search against a different database and/or use advanced search options

99777

cd06170

LuxR_C_like

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-...

true

false

true

2e-11

65.63

100.00

1,446,0,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFALR 503
cd06170        1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

cl10457

142561

LuxR_C_like

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-...

28958

cd00077

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

true

false

true

145

4e-08

55.08

99.31

3,268,0,49,324,49,25,349,81,63

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 269 PNRAGHSSGVAELAGSAASCLGLPAVDVAASRRAGYLHDIGLHGVPSTIldkpgalSATEWERVRVSSYYTERVLAQPAP 348
cd00077        1 EHRFEHSLRVAQLARRLAEELGLSEEDIELLRLAALLHDIGKPGTPDAI-------TEEESELEKDHAIVGAEILRELLL 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119717534 349 L-------ARIGAIASYTNERMDGSGYHRGASGASIPMAGRVLAAACALRTLTEPRVGRPPKSVKDAATEL 412
cd00077       74 EeviklidELILAVDASHHERLDGLGYPDGLKGEEITLEARIVKLADRLDALRRDSREKRRRIAEEDLEEL 144

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

128698

smart00421

HTH_LUXR

helix_turn_helix, Lux Regulon

false

6e-11

64.08

94.83

1,446,3,55

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFA 501
smart00421     4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58

cl10457

142561

LuxR_C_like

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-...

-1

32632

COG2771

CsgD

DNA-binding HTH domain-containing proteins [Transcription]

false

1e-09

59.61

93.85

1,446,4,61

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFALRNGLL 507
COG2771        5 LTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI 65

cl10457

142561

LuxR_C_like

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-...

-1

109261

pfam00196

GerE

Bacterial regulatory proteins, luxR family

false

1e-08

56.42

94.83

1,446,3,55

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFA 501
pfam00196      4 LSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA 58

cl10457

142561

LuxR_C_like

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-...

-1

129378

TIGR00277

HDIG

uncharacterized domain HDIG

false

0.002

39.62

41.25

2,273,7,17,293,24,16

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 119717534 274 HSSGVAELAGSAASCLGlpaVDVAASRRAGYLHDIG 309
TIGR00277      8 HSLEVAKLAEALARELG---LDVELARRGALLHDIG 40

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

32388

COG2206

c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]

false

true

false

344

8e-31

130.26

48.26

3,264,142,81,345,224,68,414,292,16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 265 DLRSPNRAGHSSGVAELAGSAASCLGLPAVDVAASRRAGYLHDIGLHGVPSTILDKPGALSATEWERVRVSSYYTERVLA 344
COG2206      143 KAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDILK 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 345 Q-PAPLARIGAIASYTNERMDGSGYHRGASGASIPMAGRVLAAACALRTLTEPRVGRPPKSVKDAATELRsEVRAGRLDV 423
COG2206      223 DlPEFLESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSDRPYKKAKSPEEALEELR-KNSGGKFDP 301


                 ....*..
gi 119717534 424 DATDAVL 430
COG2206      302 KVVDAFL 308

-1

33243

COG3437

Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

Response regulator containing a CheY-like receiver domain and an HD-GYP domain [...

false

true

false

360

1e-22

102.68

43.33

3,264,179,90,354,270,61,417,331,4

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 265 DLRSPNRAGHSSGVAELAGSAASCLGLPAVDVAASRRAGYLHDIGLHGVPSTILDKPGALSATEWERVRVSSYYTERVLA 344
COG3437      180 EVRDYETGDHLERVAQYSELLAELLGLSEEEVDLIKKAAPLHDIGKVAIPDSILLKPGKLTSEEFEIMKGHPILGAEILK 259

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119717534 345 QPAPLARIGA-IASYTNERMDGSGYHRGASGASIPMAGRVLAAACALRTLTEPRVGRPPKSVKDAATELRSEvrAGRL 421
COG3437      260 SSERLMQVAAeIARHHHERWDGSGYPDGLKGDEIPLSARIVAIADVFDALVSGRPYKEAMSTEEALEIIRAQ--SGRL 335

-1

32379

COG2197

CitB

Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain...

false

true

false

211

6e-12

67.67

29.86

1,446,148,63

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFALRNGLLDP 509
COG2197      149 LTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIRALRLGLIEA 211

-1

32733

COG2909

MalT

ATP-dependent transcriptional regulator [Transcription]

false

true

false

894

5e-07

51.07

6.82

1,446,831,61

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFALRNGLL 507
COG2909      832 LSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGLL 892

-1

139165

PRK12704

phosphodiesterase; Provisional

false

true

false

455

3e-05

45.22

12.09

3,269,269,22,294,291,16,312,307,17

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 270 NRAGHSSGVAELAGSAASCLGLpavDVAASRRAGYLHDIGLhgVPSTILDKPGALSATEW 329
PRK12704     270 NVLQHSREVAHLAGLMAAELGL---DEKLAKRAGLLHDIGK--ALDHEVEGSHVELGVEL 324

-1

135188

PRK04841

transcriptional regulator MalT; Provisional

false

true

false

903

3e-05

45.36

5.65

1,446,838,51

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTA 497
PRK04841     839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889

-1

32388

COG2206

c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]

true

false

344

7e-05

43.97

28.49

3,126,209,16,142,226,44,186,276,31

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 127 IQAHCLITSTLAERLG-LDDAVSAAVRQFFARWDGQGVPPHVGGEDLSPWVRLFHVGDITE------VYHRNGGVEAAVR 199
COG2206      210 IKKHPIYGYDILKDLPeFLESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDaltsdrPYKKAKSPEEALE 289

                         90
                 ....*....|....*...
gi 119717534 200 VARERRGRQFDPALADAF 217
COG2206      290 ELRKNSGGKFDPKVVDAF 307

-1

132362

TIGR03319

YmdA_YtgF

conserved hypothetical protein YmdA/YtgF

false

true

false

514

1e-04

43.38

6.42

2,273,332,18,294,350,15

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 119717534 274 HSSGVAELAGSAASCLGLpavDVAASRRAGYLHDIG 309
TIGR03319    333 HSIEVAHLAGIMAAELGE---DVKLAKRAGLLHDIG 365

-1

132580

TIGR03541

reg_near_HchA

LuxR family transcriptional regulatory, chaperone HchA-associated

false

true

false

232

2e-04

42.85

25.43

1,446,171,59

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFALRNG 505
TIGR03541    172 LSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKG 230

-1

137324

PRK09483

response regulator; Provisional

false

true

false

216

3e-04

41.63

29.17

1,446,148,63

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFALRNGLLDP 509
PRK09483     149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLLNA 211

-1

137598

PRK09935

transcriptional regulator FimZ; Provisional

false

true

false

210

4e-04

41.42

22.38

1,446,149,47

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACS 493
PRK09935     150 LSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHS 196

-1

139166

PRK12705

hypothetical protein; Provisional

false

true

false

485

5e-04

41.24

6.80

2,273,302,18,294,320,15

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 119717534 274 HSSGVAELAGSAASCLGLpavDVAASRRAGYLHDIG 309
PRK12705     303 HSLEVAFLAAILAALIGL---DPALAKKAGLLHDIG 335

-1

137869

PRK10403

transcriptional regulator NarP; Provisional

false

true

false

215

9e-04

40.23

26.05

1,446,153,56

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACSRSTATLFAL 502
PRK10403     154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFL 209

-1

138058

PRK10651

transcriptional regulator NarL; Provisional

false

true

false

216

0.001

40.05

34.72

2,408,138,16,445,154,59

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119717534 409 ATELRSEVRAGRLDVDatdavlsaagaggrrrvagpaGLTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAK 488
PRK10651     139 AASLRANRATTERDVN---------------------QLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKK 197

                         90
                 ....*....|....*.
gi 119717534 489 TGACSRSTATLFALRN 504
PRK10651     198 MKLKSRVEAAVWVHQE 213

-1

134107

PRK00106

hypothetical protein; Provisional

false

true

false

535

0.003

38.72

6.17

2,273,353,17,293,370,16

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 119717534 274 HSSGVAELAGSAASCLGlpaVDVAASRRAGYLHDIG 309
PRK00106     354 HSVEVGKLAGILAGELG---ENVALARRAGFLHDMG 386

-1

34204

COG4566

TtrR

Response regulator [Signal transduction mechanisms]

false

true

false

202

0.005

37.91

23.27

1,446,142,47

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 119717534 447 LTQREVEVLVLIARGVATNEVAARLGVSRKTAATHIERIYAKTGACS 493
COG4566      143 LTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189

-1

31608

COG1418

Predicted HD superfamily hydrolase [General function prediction only]

false

true

false

222

0.010

36.97

17.57

2,267,33,23,293,56,16

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 119717534 268 SPNRAGHSSGVAELAGSAASCLGlpaVDVAASRRAGYLHDIG 309
COG1418       34 GQHVLEHSLRVAYLAYRIAEEEG---VDPDLALRAALLHDIG 72

-1

DNA binding residues	0	16	16	true	99777	cd06170	LuxR_C_like
dimerization interface	1	9	9	true	99777	cd06170	LuxR_C_like
Zn2+ binding site	0	4	4	true	28958	cd00077	HDc
Mg2+ binding site	1	1	1	true	28958	cd00077	HDc