NCBI Conserved Domain Search

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Conserved domains on [gi\|120403052\|ref\|YP_952881.1\|]
metal dependent phosphohydrolase [Mycobacterium vanbaalenii PYR-1]

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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

71.41

100.00

1,457,0,57

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 120403052 458 LTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALN 514
cd06170        1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 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

8e-14

73.71

93.10

1,454,0,54

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 120403052 455 PGGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGA 508
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

4e-11

64.89

94.83

1,457,3,55

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 120403052 458 LTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFA 512
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

4e-11

65.01

100.00

1,453,0,65

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 120403052 454 RPGGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNHGLV 518
COG2771        1 RTADLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI 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

2e-04

42.37

60.69

3,310,31,18,335,49,25,360,81,38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 311 RRAGHLHDLGRIGVSNQIwskpsslTARELERVRLHPYLTVRILSQVGGL-------DAVAQVAGNHHEYLDGSGYPRGL 383
cd00077       32 RLAALLHDIGKPGTPDAI-------TEEESELEKDHAIVGAEILRELLLEeviklidELILAVDASHHERLDGLGYPDGL 104

                         90
                 ....*....|....*
gi 120403052 384 PAAALSLPDRLLAAA 398
cd00077      105 KGEEITLEARIVKLA 119

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

32388

COG2206

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

true

false

344

1e-28

122.94

51.16

3,274,141,86,360,228,65,426,293,24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 275 VDLKCPFTLGHSRAVAELAAGAAAVVGLDADTVTVVRRAGHLHDLGRIGVSNQIWSKPSSLTARELERVRLHPYLTVRIL 354
COG2206      142 IKAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDIL 221

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 355 SQVGGL-DAVAQVAGNHHEYLDGSGYPRGLPAAALSLPDRLLAAAVAYQSALEPRPYRDPLPATSAAARLRErVREGRLD 433
COG2206      222 KDLPEFlESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSDRPYKKAKSPEEALEELRK-NSGGKFD 300

                        170
                 ....*....|....*..
gi 120403052 434 EVAVEAVLQAAGHRARG 450
COG2206      301 PKVVDAFLKALSKYPIG 317

-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-18

88.82

36.11

4,312,216,45,357,262,68,427,330,5,432,336,10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 313 AGHLHDLGRIGVSNQIWSKPSSLTARELERVRLHPYLTVRILSQV-GGLDAVAQVAGNHHEYLDGSGYPRGLPAAALSLP 391
COG3437      217 AAPLHDIGKVAIPDSILLKPGKLTSEEFEIMKGHPILGAEILKSSeRLMQVAAEIARHHHERWDGSGYPDGLKGDEIPLS 296

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 120403052 392 DRLLAAAVAYQSALEPRPYRDPLPATSAAARLRErvREGRL-DEVAVEAVLQ 442
COG3437      297 ARIVAIADVFDALVSGRPYKEAMSTEEALEIIRA--QSGRLfDPKLVEAFIQ 346

-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-15

78.84

39.81

1,436,127,84

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 437 VEAVLQAAGHRARGHSPRPGGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNHG 516
COG2197      128 IARKLAGLLPSSSAEAPLAELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIRALRLG 207


                 ....
gi 120403052 517 LVAP 520
COG2197      208 LIEA 211

-1

132065

TIGR03020

EpsA

transcriptional regulator EpsA

false

true

false

247

6e-08

54.40

30.77

2,439,165,16,455,188,53

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 120403052 440 VLQAAGHRARGHSPRP-------GGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGA 508
TIGR03020    166 ALRRVLFLPNQHRTRPlgerhsaGLITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241

-1

138058

PRK10651

transcriptional regulator NarL; Provisional

false

true

false

216

5e-07

51.22

27.31

1,456,154,59

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 120403052 457 GLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNH 515
PRK10651     155 QLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQE 213

-1

32733

COG2909

MalT

ATP-dependent transcriptional regulator [Transcription]

false

true

false

894

6e-07

50.69

5.82

1,456,830,52

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 120403052 457 GLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGA 508
COG2909      831 PLSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQA 882

-1

34204

COG4566

TtrR

Response regulator [Signal transduction mechanisms]

false

true

false

202

2e-06

49.08

34.65

1,434,119,70

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 435 VAVEAVLQAAGHRARGHSPRPGGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATN 504
COG4566      120 LARDASRRAEADRQAAIRARLATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189

-1

137869

PRK10403

transcriptional regulator NarP; Provisional

false

true

false

215

5e-06

47.93

46.98

4,417,110,13,430,124,19,449,144,6,455,151,60

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120403052 418 SAAARLRERVREG-RLDEVAVEAVLQAAGHRAR-GHSPRP-GGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVE 494
PRK10403     111 SDPEVLLEAIRAGaKGSKVFSERVNQYLREREMfGAEEDPfSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIR 190

                         90       100
                 ....*....|....*....|.
gi 120403052 495 RTYAKIGATNRIGASMFALNH 515
PRK10403     191 NLLRKLNVRSRVAATILFLQQ 211

-1

135188

PRK04841

transcriptional regulator MalT; Provisional

false

true

false

903

2e-05

46.13

5.65

2,450,835,3,457,838,48

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 120403052 451 HSPrpggLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNR 505
PRK04841     836 TSP----LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHR 886

-1

137598

PRK09935

transcriptional regulator FimZ; Provisional

false

true

false

210

3e-05

45.65

29.05

1,457,149,61

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 120403052 458 LTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNHGLV 518
PRK09935     150 LSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHELL 210

-1

137688

PRK10100

DNA-binding transcriptional regulator CsgD; Provisional

false

true

false

216

5e-05

44.55

26.85

1,457,155,58

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 120403052 458 LTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNH 515
PRK10100     156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213

-1

132580

TIGR03541

reg_near_HchA

LuxR family transcriptional regulatory, chaperone HchA-associated

false

true

false

232

6e-05

44.39

27.16

1,453,167,63

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 120403052 454 RPGGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNHG 516
TIGR03541    168 EAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKG 230

-1

139792

PRK13719

conjugal transfer transcriptional regulator TraJ; Provisional

false

true

false

220

3e-04

42.05

26.82

1,461,149,59

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 120403052 462 EIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRIGASMFALNHGLVAP 520
PRK13719     150 QYDVFILYSFGFSHNSIASLLNITNGSSKNKISEILKFFGISSRDELLIILHTSEMISP 208

-1

136118

PRK06930

positive control sigma-like factor; Validated

false

true

false

170

0.002

39.32

32.35

3,457,114,11,468,126,33,503,159,10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 120403052 458 LTPREIEVLCL-VARGASNKEIAATLGISGKTARNHVERTYAKIGatNRIGASMFAL 513
PRK06930     115 LTEREKEVYLMhRGYGLSYSEIAAYLNIKKSTVQSMIERAEKKIA--KQINESLFCM 169

-1

137244

PRK09390

fixJ

response regulator FixJ; Provisional

false

true

false

202

0.005

38.08

37.13

2,435,113,17,452,136,52

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 120403052 436 AVEAVLQAAGHRARGHS------PRPGGLTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATN 504
PRK09390     114 AIERALAQAPAAAKSEAvaadirARIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188

-1

132030

TIGR02985

Sig70_bacteroi1

RNA polymerase sigma-70 factor, Bacteroides expansion family 1

false

true

false

161

0.006

37.56

24.22

2,460,118,9,470,127,30

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 120403052 461 REIEVLCLVaRGASNKEIAATLGISGKTARNHVERTYAKI 500
TIGR02985    119 RKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKEL 157

-1

137846

PRK10360

DNA-binding transcriptional activator UhpA; Provisional

false

true

false

196

0.008

37.31

25.00

1,457,137,49

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 120403052 458 LTPREIEVLCLVARGASNKEIAATLGISGKTARNHVERTYAKIGATNRI 506
PRK10360     138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDV 186

-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