NCBI Conserved Domain Search

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Conserved domains on [gi\|119714219\|ref\|YP_919361.1\|]
metal-dependent phosphohydrolase [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

1e-12

70.26

100.00

1,453,0,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119714219 454 LSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAME 510
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

8e-11

63.56

87.59

1,275,1,127

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 276 YTLGHSSGTSELAELAGRAIGLDDPAVGNLRRAALLHDLGRVGVSSGIWDKPGALTRSELEQVRLHPYHTERILACSPVL 355
cd00077        2 HRFEHSLRVAQLARRLAEELGLSEEDIELLRLAALLHDIGKPGTPDAITEEESELEKDHAIVGAEILRELLLEEVIKLID 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 119714219 356 APLGRIAGLHHERLDGSGYHHGLAAAAIPIEARVLAAADTFQTLTQD 402
cd00077       82 ELILAVDASHHERLDGLGYPDGLKGEEITLEARIVKLADRLDALRRD 128

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

128698

smart00421

HTH_LUXR

helix_turn_helix, Lux Regulon

false

1e-13

73.33

100.00

1,450,0,58

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 119714219 451 PSGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYA 508
smart00421     1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 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

2e-10

62.58

94.83

1,453,3,55

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 119714219 454 LSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYA 508
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

32632

COG2771

CsgD

DNA-binding HTH domain-containing proteins [Transcription]

false

8e-10

60.38

98.46

1,450,1,64

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119714219 451 PSGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAMEHDLL 514
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

128747

smart00471

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif.

false

124

1e-06

49.98

92.74

5,275,3,27,304,30,26,338,56,16,354,76,22,382,98,20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 276 YTLGHSSGTSELAELAGRAIGLDDPAVgnLRRAALLHDLGRVGVSSGIWDKPGALtrseleqvRLHPYHTERILACSPV- 354
smart00471     4 HVFEHSLRVAQLAAALAEELGLLDIEL--LLLAALLHDIGKPGTPDSFLVKTSVL--------EDHHFIGAEILLEEEEp 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 119714219 355 ---LAPLGRIAGLHHERLDGSGYHHglaaaaIPIEARVLAAADTFQTLTQD 402
smart00471    74 rilEEILATAILSHHERPDGLRGEP------ITLEARIVKVADRLDALRRD 118

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

110919

pfam01966

HD domain

false

108

6e-06

47.62

100.00

5,276,0,22,301,22,18,326,40,33,359,74,15,380,89,19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 277 TLGHSSGTSELAELAGRAIGLDdpaVGNLRRAALLHDLGRVGVssgiwdkPGALTRSELEQVRLHPYHTERILACSPVLA 356
pfam01966      1 VLEHSLRVALLARELAEELGLD---PELLLLAALLHDIGKDPF-------GFLEKLEDFGIFKSHSVVGAEILRELEKRL 70

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 119714219 357 PLG-RIAGLHHERLDGSGYhhglaaAAIPIEARVLAAADTFQTL 399
pfam01966     71 GVDlELILEHHESWEGAGY------EPISLEARIVKLADRLDAL 108

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

2e-34

141.81

50.87

3,268,140,81,349,222,53,403,275,40

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 269 MVDLKSTYTLGHSSGTSELAELAGRAIGLDDPAVGNLRRAALLHDLGRVGVSSGIWDKPGALTRSELEQVRLHPYHTERI 348
COG2206      141 DIKAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDI 220

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 349 L-ACSPVLAPLGRIAGLHHERLDGSGYHHGLAAAAIPIEARVLAAADTFQTLTQDrPHRAAHPPERAAERLAEEARAGRF 427
COG2206      221 LkDLPEFLESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSD-RPYKKAKSPEEALEELRKNSGGKF 299

                        170
                 ....*....|....*.
gi 119714219 428 DTDSVRAVVEAAGEQP 443
COG2206      300 DPKVVDAFLKALSKYP 315

-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

7e-24

106.92

46.39

4,240,143,13,254,156,12,266,175,86,352,262,48

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 241 QEVLEVEPAPVRRiRSGELDRVARCF-------ADMVDLKSTYTLGHSSGTSELAELAGRAIGLDDPAVGNLRRAALLHD 313
COG3437      144 DQNLYLELQELRR-RTEELAQIEDNLdetleelAALLEVRDYETGDHLERVAQYSELLAELLGLSEEEVDLIKKAAPLHD 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 314 LGRVGVSSGIWDKPGALTRSELEQVRLHPYHTERILACS-PVLAPLGRIAGLHHERLDGSGYHHGLAAAAIPIEARVLAA 392
COG3437      223 IGKVAIPDSILLKPGKLTSEEFEIMKGHPILGAEILKSSeRLMQVAAEIARHHHERWDGSGYPDGLKGDEIPLSARIVAI 302


                 ....*...
gi 119714219 393 ADTFQTLT 400
COG3437      303 ADVFDALV 310

-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

2e-13

72.29

41.71

2,426,123,22,450,145,66

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 427 FDTDSVRAVVEAAGEQPAPVRGnwPSGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAAL 506
COG2197      124 LPPDIARKLAGLLPSSSAEAPL--AELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAI 201

                         90
                 ....*....|
gi 119714219 507 YAMEHDLLRP 516
COG2197      202 RALRLGLIEA 211

-1

137598

PRK09935

transcriptional regulator FimZ; Provisional

false

true

false

210

4e-10

61.45

29.05

1,453,149,61

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119714219 454 LSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAMEHDLL 514
PRK09935     150 LSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHELL 210

-1

32733

COG2909

MalT

ATP-dependent transcriptional regulator [Transcription]

false

true

false

894

2e-08

56.08

7.05

1,452,830,63

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119714219 453 GLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAMEHDLLR 515
COG2909      831 PLSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGLLM 893

-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

2e-08

55.69

22.78

3,156,271,33,189,309,9,198,319,34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 157 IAQQFERWDGTGGPGGLAGVEITLAARVSEVAT-----QALLVHQEA-GVDAVMSMLRDRSGSWFDPSVVEACARHGADL 230
COG3437      272 ARHHHERWDGSGYPDGLKGDEIPLSARIVAIADvfdalVSGRPYKEAmSTEEALEIIRAQSGRLFDPKLVEAFIQVEDEI 351


                 ..
gi 119714219 231 LR 232
COG3437      352 ID 353

-1

132065

TIGR03020

EpsA

transcriptional regulator EpsA

false

true

false

247

6e-08

54.40

23.08

1,452,189,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119714219 453 GLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAM 509
TIGR03020    190 LITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAI 246

-1

138058

PRK10651

transcriptional regulator NarL; Provisional

false

true

false

216

9e-08

53.53

28.70

1,451,153,62

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119714219 452 SGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAMEHDL 513
PRK10651     154 NQLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI 215

-1

32388

COG2206

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

false

true

false

344

1e-07

53.22

22.09

4,156,234,33,189,269,4,193,276,5,198,282,28

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119714219 157 IAQQFERWDGTGGPGGLAGVEITLAARVSEVAT--QALL---VHQEA-GVDAVMSMLRDRSGSWFDPSVVEACARH 226
COG2206      235 ALRHHERWDGTGYPRGLKGEEIPLEARIIAVADvyDALTsdrPYKKAkSPEEALEELRKNSGGKFDPKVVDAFLKA 310

-1

137869

PRK10403

transcriptional regulator NarP; Provisional

false

true

false

215

2e-06

49.47

32.56

2,436,141,10,451,151,60

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 119714219 437 EAAGEQPAPVrgnwpSGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAMEH 511
PRK10403     142 EMFGAEEDPF-----SVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211

-1

137688

PRK10100

DNA-binding transcriptional regulator CsgD; Provisional

false

true

false

216

4e-05

44.55

26.85

1,453,155,58

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 119714219 454 LSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYAMEH 511
PRK10100     156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213

-1

135188

PRK04841

transcriptional regulator MalT; Provisional

false

true

false

903

7e-05

43.82

6.31

1,451,836,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119714219 452 SGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAAALYA 508
PRK04841     837 SPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQLA 893

-1

132580

TIGR03541

reg_near_HchA

LuxR family transcriptional regulatory, chaperone HchA-associated

false

true

false

232

8e-05

44.00

25.86

1,444,162,60

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 119714219 445 PVRGNWPSGLSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAAA 504
TIGR03541    163 APLLREAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQA 222

-1

34204

COG4566

TtrR

Response regulator [Signal transduction mechanisms]

false

true

false

202

2e-04

42.15

24.75

1,453,142,50

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 119714219 454 LSDREVEVLRLVAKGLSNQEVAQTLVISRRTAEHHVQHVYAKIGTSTRAA 503
COG4566      143 LTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAE 192

-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