NCBI Conserved Domain Search

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Conserved domains on [gi\|119866977\|ref\|YP_936929.1\|]
metal dependent phosphohydrolase [Mycobacterium sp. KMS]

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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

5e-13

71.03

98.25

1,462,1,56

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALE 518
cd06170        2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

cl10457

142561

LuxR_C_like

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

128698

smart00421

HTH_LUXR

helix_turn_helix, Lux Regulon

false

1e-13

73.33

93.10

1,462,4,54

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYA 516
smart00421     5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58

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

7e-12

67.20

93.10

1,462,4,54

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYA 516
pfam00196      5 SPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA 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

6e-11

64.24

92.31

1,462,5,60

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEHGLL 522
COG2771        6 TPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI 65

cl10457

142561

LuxR_C_like

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

-1

28958

cd00077

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

true

false

true

145

1e-04

43.53

60.00

3,313,29,23,343,52,24,367,83,33

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 314 LTRRAGHVHDIGRIGVSNQVWSKgsalstaEFERVRLHPYLTERILRQVPGLAQ-------VAAVASNHHERLDGTGYPR 386
cd00077       30 LLRLAALLHDIGKPGTPDAITEE-------ESELEKDHAIVGAEILRELLLEEViklidelILAVDASHHERLDGLGYPD 102

                         90
                 ....*....|....
gi 119866977 387 GLSARELTMPDRVL 400
cd00077      103 GLKGEEITLEARIV 116

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

32388

COG2206

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

false

true

false

344

8e-24

106.76

41.28

2,279,141,86,365,228,55

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 280 VDLKCPFTAGHSRAVAALAADAATALGLDGEAVALTRRAGHVHDIGRIGVSNQVWSKGSALSTAEFERVRLHPYLTERIL 359
COG2206      142 IKAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDIL 221

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119866977 360 RQVPGL-AQVAAVASNHHERLDGTGYPRGLSARELTMPDRVLAAAVAFQAACEPRPYRAQMT 420
COG2206      222 KDLPEFlESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSDRPYKKAKS 283

-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-16

82.27

43.33

2,265,164,105,370,270,50

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 266 ASGLDALLIALGDFVDLKCPFTAGHSRAVAALAADAATALGLDGEAVALTRRAGHVHDIGRIGVSNQVWSKGSALSTAEF 345
COG3437      165 EDNLDETLEELAALLEVRDYETGDHLERVAQYSELLAELLGLSEEEVDLIKKAAPLHDIGKVAIPDSILLKPGKLTSEEF 244

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119866977 346 ERVRLHPYLTERILRQVPGLAQVAA-VASNHHERLDGTGYPRGLSARELTMPDRVLAAAVAFQAACEPRPYRAQMT 420
COG3437      245 EIMKGHPILGAEILKSSERLMQVAAeIARHHHERWDGSGYPDGLKGDEIPLSARIVAIADVFDALVSGRPYKEAMS 320

-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

3e-14

75.38

28.44

1,462,149,60

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEHGLL 522
COG2197      150 TPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIRALRLGLI 209

-1

32388

COG2206

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

true

false

344

8e-10

60.54

29.36

3,142,207,6,148,214,56,204,276,32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 143 RLIHSH-CASAAMLAERIGLDDDVRRALGFTFERFDGGGLPEGASGDAIPIEMRVAQFADLLE------VHHRGYGVEGA 215
COG2206      208 EIIKKHpIYGYDILKDLPEFLESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDaltsdrPYKKAKSPEEA 287

                         90       100
                 ....*....|....*....|.
gi 119866977 216 VAMARNRRGGQFDPAVVDAFV 236
COG2206      288 LEELRKNSGGKFDPKVVDAFL 308

-1

32733

COG2909

MalT

ATP-dependent transcriptional regulator [Transcription]

false

true

false

894

2e-09

58.78

6.94

1,462,832,62

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEHGLLGR 524
COG2909      833 SQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGLLMG 894

-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-08

56.07

50.83

7,22,169,41,69,210,6,97,216,25,122,242,24,154,266,10,173,276,31,204,313,39

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977  23 EVLAALSVAIDLGLGQPAEHMLRSALIATRLADRLGLTRAQrdcvyyATLIMWigchadsheyarwfgddiavrrASYLV 102
COG3437      170 ETLEELAALLEVRDYETGDHLERVAQYSELLAELLGLSEEE------VDLIKK----------------------AAPLH 221

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119866977 103 DWSGLPYQRFLLANIAHGEP-LLQRLRTATALYADARGNISRLIHshcasaamLAERIGLDDDvrralgftfERFDGGGL 181
COG3437      222 DIGKVAIPDSILLKPGKLTSeEFEIMKGHPILGAEILKSSERLMQ--------VAAEIARHHH---------ERWDGSGY 284

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119866977 182 PEGASGDAIPIEMRVAQFADLLE------VHHRGYGVEGAVAMARNRRGGQFDPAVVDAFVTDPDALL 243
COG3437      285 PDGLKGDEIPLSARIVAIADVFDalvsgrPYKEAMSTEEALEIIRAQSGRLFDPKLVEAFIQVEDEII 352

-1

138058

PRK10651

transcriptional regulator NarL; Provisional

false

true

false

216

2e-07

52.37

26.39

1,462,156,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEH 519
PRK10651     157 TPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQE 213

-1

137869

PRK10403

transcriptional regulator NarP; Provisional

false

true

false

215

4e-07

51.40

26.51

1,462,154,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEH 519
PRK10403     155 TERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211

-1

137688

PRK10100

DNA-binding transcriptional regulator CsgD; Provisional

false

true

false

216

5e-07

51.10

26.39

1,462,156,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEH 519
PRK10100     157 THREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213

-1

132065

TIGR03020

EpsA

transcriptional regulator EpsA

false

true

false

247

9e-07

50.55

20.24

1,462,191,50

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAA 512
TIGR03020    192 TAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241

-1

137598

PRK09935

transcriptional regulator FimZ; Provisional

false

true

false

210

2e-06

49.12

27.62

1,464,152,58

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 119866977 465 REAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEHGLL 522
PRK09935     153 REVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHELL 210

-1

135188

PRK04841

transcriptional regulator MalT; Provisional

false

true

false

903

7e-05

44.20

5.98

1,462,839,54

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYA 516
PRK04841     840 TQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQLA 893

-1

34204

COG4566

TtrR

Response regulator [Signal transduction mechanisms]

false

true

false

202

6e-04

40.99

22.77

1,462,143,46

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSN 508
COG4566      144 TPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189

-1

132580

TIGR03541

reg_near_HchA

LuxR family transcriptional regulatory, chaperone HchA-associated

false

true

false

232

0.001

40.15

25.00

1,462,172,58

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEHG 520
TIGR03541    173 SEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKG 230

-1

137737

PRK10188

DNA-binding transcriptional activator SdiA; Provisional

false

true

false

240

0.002

39.41

24.17

1,464,182,58

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 119866977 465 REAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRVAASLYALEHGLL 522
PRK10188     183 REKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240

-1

137846

PRK10360

DNA-binding transcriptional activator UhpA; Provisional

false

true

false

196

0.005

38.08

24.49

1,462,138,48

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 119866977 463 TAREAEVLCLVAQGATNKEIAARLVISEKTARNHVERTYAKIGVSNRV 510
PRK10360     139 TKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDV 186

-1

136118

PRK06930

positive control sigma-like factor; Validated

false

true

false

170

0.009

37.01

31.76

3,462,115,10,472,126,33,507,159,10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 119866977 463 TAREAEVLCL-VAQGATNKEIAARLVISEKTARNHVERTYAKIGvsNRVAASLYAL 517
PRK06930     116 TEREKEVYLMhRGYGLSYSEIAAYLNIKKSTVQSMIERAEKKIA--KQINESLFCM 169

-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	2	4	true	28958	cd00077	HDc
Mg2+ binding site	1	1	1	true	28958	cd00077	HDc