NCBI Conserved Domain Search

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Conserved domains on [gi\|111023879\|ref\|YP_706851.1\|]
hypothetical protein RHA1_ro06927 [Rhodococcus jostii RHA1]

Graphical summary show options »	Show site features Horizontal zoom: ×	?



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-15

79.50

100.00

1,459,0,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAID 516
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-09

58.17

90.34

1,281,0,131

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 282 PFTLGHSRGVANLVAGAARHLGMSPSDITHLYRAGLVHSLGKMGVSNQIWEKKGPLTTTEWERVRMYPDLTGRILSRVNG 361
cd00077        1 EHRFEHSLRVAQLARRLAEELGLSEEDIELLRLAALLHDIGKPGTPDAITEEESELEKDHAIVGAEILRELLLEEVIKLI 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 111023879 362 LESVVSVAMKHRERIDGSGFPRGIAGAELTAKDRLLAAADAYQRLLEPRPH 412
cd00077       81 DELILAVDASHHERLDGLGYPDGLKGEEITLEARIVKLADRLDALRRDSRE 131

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

128698

smart00421

HTH_LUXR

helix_turn_helix, Lux Regulon

false

1e-16

82.96

93.10

1,456,0,54

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 111023879 457 PAGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQA 510
smart00421     1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQA 54

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

3e-14

75.29

87.93

1,459,3,51

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQA 510
pfam00196      4 LSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVEL 54

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-12

70.01

98.46

1,456,1,64

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 111023879 457 PAGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAIDRGLV 520
COG2771        2 TADLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI 65

cl10457

142561

LuxR_C_like

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

-1

110919

pfam01966

HD domain

false

108

6e-04

41.07

100.00

5,283,0,21,307,21,20,334,41,37,371,79,10,387,89,19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 284 TLGHSRGVANLVAGAARHLGMspsDITHLYRAGLVHSLGKMGVSnqiwekkGPLTTTEWERVRMYPDLTGRILSRVNGLE 363
pfam01966      1 VLEHSLRVALLARELAEELGL---DPELLLLAALLHDIGKDPFG-------FLEKLEDFGIFKSHSVVGAEILRELEKRL 70

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 111023879 364 SVVSVAMK-HRERIDGSGFprgiagAELTAKDRLLAAADAYQRL 406
pfam01966     71 GVDLELILeHHESWEGAGY------EPISLEARIVKLADRLDAL 108

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

128747

smart00471

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif.

false

124

0.001

39.97

95.16

5,283,4,20,305,24,42,350,66,9,361,75,13,379,88,34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 284 TLGHSRGVANLVAGAARHLGmsPSDITHLYRAGLVHSLGKMGVSNQIWEKKGPLTTTEWERVRMypdLTGRILSRVngLE 363
smart00471     5 VFEHSLRVAQLAAALAEELG--LLDIELLLLAALLHDIGKPGTPDSFLVKTSVLEDHHFIGAEI---LLEEEEPRI--LE 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 111023879 364 SVVSVAMKHREridgsGFPRGIAGAELTAKDRLLAAADAYQRLLEPRPHR 413
smart00471    78 EILATAILSHH-----ERPDGLRGEPITLEARIVKVADRLDALRRDRRYR 122

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

7e-33

137.19

44.77

2,276,141,86,362,228,67

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 277 VDLKSPFTLGHSRGVANLVAGAARHLGMSPSDITHLYRAGLVHSLGKMGVSNQIWEKKGPLTTTEWERVRMYPDLTGRIL 356
COG2206      142 IKAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDIL 221

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 111023879 357 SRVNGL-ESVVSVAMKHRERIDGSGFPRGIAGAELTAKDRLLAAADAYQRLLEPRPHRLALDPRGAADRLKEEA 429
COG2206      222 KDLPEFlESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSDRPYKKAKSPEEALEELRKNS 295

-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

2e-25

112.31

48.89

2,256,158,105,361,264,70

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 257 RDRTLTAEESDELLGAMADFVDLKSPFTLGHSRGVANLVAGAARHLGMSPSDITHLYRAGLVHSLGKMGVSNQIWEKKGP 336
COG3437      159 EELAQIEDNLDETLEELAALLEVRDYETGDHLERVAQYSELLAELLGLSEEEVDLIKKAAPLHDIGKVAIPDSILLKPGK 238

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 337 LTTTEWERVRMYPDLTGRILSRVNG-LESVVSVAMKHRERIDGSGFPRGIAGAELTAKDRLLAAADAYQRLLEPRPHRLA 415
COG3437      239 LTSEEFEIMKGHPILGAEILKSSERlMQVAAEIARHHHERWDGSGYPDGLKGDEIPLSARIVAIADVFDALVSGRPYKEA 318

                        170
                 ....*....|....*.
gi 111023879 416 LDPRGAADRLKEEART 431
COG3437      319 MSTEEALEIIRAQSGR 334

-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

5e-17

84.24

34.60

1,447,136,73

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 111023879 448 QRVSRRTPWPAGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAIDRGLV 520
COG2197      137 PSSSAEAPLAELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIRALRLGLI 209

-1

32733

COG2909

MalT

ATP-dependent transcriptional regulator [Transcription]

false

true

false

894

1e-11

66.10

6.82

1,458,830,61

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 111023879 459 GLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAIDRGL 519
COG2909      831 PLSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGL 891

-1

132065

TIGR03020

EpsA

transcriptional regulator EpsA

false

true

false

247

3e-10

62.11

23.89

2,446,182,7,458,189,52

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 111023879 447 GQRVSRRtpwpaGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQA 510
TIGR03020    183 GERHSAG-----LITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241

-1

137688

PRK10100

DNA-binding transcriptional regulator CsgD; Provisional

false

true

false

216

2e-09

59.19

24.54

1,457,153,53

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 111023879 458 AGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQA 510
PRK10100     154 ALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQA 206

-1

138058

PRK10651

transcriptional regulator NarL; Provisional

false

true

false

216

8e-09

57.38

25.00

1,457,153,54

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 111023879 458 AGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQAS 511
PRK10651     154 NQLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAA 207

-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 [...

true

false

360

4e-08

54.92

24.72

3,158,265,10,168,276,31,199,313,41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 159 QVGKALAYVF-ERWDGRGLPNGCRGEGIPIEIHISHVADVVE------VHLRTGGLGHAKEVLRSRRGSQFSPAVVEVFE 231
COG3437      266 QVAAEIARHHhERWDGSGYPDGLKGDEIPLSARIVAIADVFDalvsgrPYKEAMSTEEALEIIRAQSGRLFDPKLVEAFI 345


                 ....*....
gi 111023879 232 RDAAAIVDG 240
COG3437      346 QVEDEIIDI 354

-1

32388

COG2206

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

false

true

false

344

1e-07

53.22

45.93

7,36,151,36,98,187,11,116,198,3,119,205,4,139,209,4,143,214,56,199,276,33

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879  37 HMLRSSLIATRIAERMGLDPEQQATVYYANLVGWIGchadshelsalfgddiafradtyavdMTGLPFLRLMTshvgrgl 116
COG2206      152 HSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIG--------------------------KIGIPDSILNK------- 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111023879 117 PGW----ERGIraavflvaargrvatlIHSH-CSSAGVLSDRMGLDGQVGKALAYVFERWDGRGLPNGCRGEGIPIEIHI 191
COG2206      199 PGKlteeEFEI----------------IKKHpIYGYDILKDLPEFLESVRAVALRHHERWDGTGYPRGLKGEEIPLEARI 262

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 111023879 192 SHVADVVE------VHLRTGGLGHAKEVLRSRRGSQFSPAVVEVFER 232
COG2206      263 IAVADVYDaltsdrPYKKAKSPEEALEELRKNSGGKFDPKVVDAFLK 309

-1

135188

PRK04841

transcriptional regulator MalT; Provisional

false

true

false

903

3e-07

51.91

6.09

2,451,834,4,459,838,51

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 111023879 452 RRTPwpagLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQA 510
PRK04841     835 RTSP----LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889

-1

137598

PRK09935

transcriptional regulator FimZ; Provisional

false

true

false

210

4e-07

51.43

22.38

1,459,149,47

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNN 506
PRK09935     150 LSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHS 196

-1

137869

PRK10403

transcriptional regulator NarP; Provisional

false

true

false

215

3e-06

48.70

24.65

1,459,153,53

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASL 512
PRK10403     154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATI 206

-1

132580

TIGR03541

reg_near_HchA

LuxR family transcriptional regulatory, chaperone HchA-associated

false

true

false

232

3e-06

48.63

25.43

1,459,171,59

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAIDRG 518
TIGR03541    172 LSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKG 230

-1

34204

COG4566

TtrR

Response regulator [Signal transduction mechanisms]

false

true

false

202

6e-06

47.54

24.26

1,457,140,49

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 111023879 458 AGLTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNN 506
COG4566      141 ATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189

-1

137737

PRK10188

DNA-binding transcriptional activator SdiA; Provisional

false

true

false

240

2e-04

42.88

25.42

1,459,179,61

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAIDRGLV 520
PRK10188     180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240

-1

136118

PRK06930

positive control sigma-like factor; Validated

false

true

false

170

0.005

37.78

31.18

3,459,114,11,470,126,27,499,153,14

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 111023879 460 LTDREVEILRL-VAQGRSNREIAADLFIAEKTARNHVERvyAKLGVNNRTQASLA 513
PRK06930     115 LTEREKEVYLMhRGYGLSYSEIAAYLNIKKSTVQSMIER--AEKKIAKQINESLF 167

-1

137846

PRK10360

DNA-binding transcriptional activator UhpA; Provisional

false

true

false

196

0.006

37.70

29.08

1,459,137,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 111023879 460 LTDREVEILRLVAQGRSNREIAADLFIAEKTARNHVERVYAKLGVNNRTQASLAAID 516
PRK10360     138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFD 194

-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