NCBI Conserved Domain Search

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Conserved domains on [gi\|41409450\|ref\|NP_962286.1\|]
hypothetical protein MAP3352c [Mycobacterium avium subsp. paratuberculosis K-10]

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

6e-13

71.03

100.00

1,455,0,57

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 41409450 456 LTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQ 512
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

4e-14

74.87

100.00

1,452,0,58

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 41409450 453 PDGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYA 510
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

4e-12

67.98

98.28

1,453,1,57

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 41409450 454 DGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYA 510
pfam00196     2 DSLSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA 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

7e-11

63.85

100.00

1,451,0,65

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41409450 452 RPDGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQHGLV 516
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

1e-04

43.14

78.62

4,305,29,23,335,52,27,362,86,33,395,120,23

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 306 LTRRAGHVHDLGRIGVSNQIWSRpgplsgsQFERVRLHPYLTVRILDQVPGLRRLAE-------VAGNHHECLDGSGYPR 378
cd00077      30 LLRLAALLHDIGKPGTPDAITEE-------ESELEKDHAIVGAEILRELLLEEVIKLidelilaVDASHHERLDGLGYPD 102

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 41409450 379 GLAGPALGMPDRILAAA-VCYQSGREPRPYREQLSEAEAAR 418
cd00077     103 GLKGEEITLEARIVKLAdRLDALRRDSREKRRRIAEEDLEE 143

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

1e-27

119.86

56.10

5,255,124,16,271,141,86,357,228,64,422,292,14,436,307,10

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 256 VDEQSLDAALVALGDF-VDLKCPFTLGHSRAVARLAGQAARAAGLDADAVALTRRAGHVHDLGRIGVSNQIWSRPGPLSG 334
COG2206     125 VAREIVKKALVALARGdIKAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTE 204

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 335 SQFERVRLHPYLTVRILDQVPGL-RRLAEVAGNHHECLDGSGYPRGLAGPALGMPDRILAAAVCYQSGREPRPYREQLSE 413
COG2206     205 EEFEIIKKHPIYGYDILKDLPEFlESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSDRPYKKAKSP 284

                       170       180       190
                ....*....|....*....|....*....|....
gi 41409450 414 AEAARRLRgRVRCGELDPVAAEA-VLHAAGQPVG 446
COG2206     285 EEALEELR-KNSGGKFDPKVVDAfLKALSKYPIG 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

89.20

46.11

2,257,164,104,361,269,61

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 258 EQSLDAALVALGDFVDLKCPFTLGHSRAVARLAGQAARAAGLDADAVALTRRAGHVHDLGRIGVSNQIWSRPGPLSGSQF 337
COG3437     165 EDNLDETLEELAALLEVRDYETGDHLERVAQYSELLAELLGLSEEEVDLIKKAAPLHDIGKVAIPDSILLKPGKLTSEEF 244

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 338 ERVRLHPYLTVRILDQVPGLRRLA-EVAGNHHECLDGSGYPRGLAGPALGMPDRILAAAVCYQSGREPRPYREQLSEAEA 416
COG3437     245 EIMKGHPILGAEILKSSERLMQVAaEIARHHHERWDGSGYPDGLKGDEIPLSARIVAIADVFDALVSGRPYKEAMSTEEA 324


                ....*.
gi 41409450 417 ARRLRG 422
COG3437     325 LEIIRA 330

-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-17

84.24

41.23

2,427,122,17,446,139,70

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 428 ELDPVAAEAVLHAAGQPvgPRPNPRPDGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGAS 507
COG2197     123 YLPPDIARKLAGLLPSS--SAEAPLAELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAA 200


                ....*....
gi 41409450 508 MYALQHGLV 516
COG2197     201 IRALRLGLI 209

-1

32733

COG2909

MalT

ATP-dependent transcriptional regulator [Transcription]

false

true

false

894

5e-09

58.01

11.63

2,398,787,40,451,827,64

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 399 QSGREPRPYREQLSEAEAARRLRGRVRCGELDPVAAEAVLhaagqpvgprpnpRPDGLTPREIEVLGHVARGASNKEIAA 478
COG2909     788 LLGELPELERHRLQRILREILQTQRQKFIHLDEEFVEGLL-------------NELPLSQRELEVLGLIAQGLSNEEIAQ 854

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 41409450 479 ALVISEKTARNHVERTYAKIGVSNRIGASMYALQHGL 515
COG2909     855 ELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGL 891

-1

137869

PRK10403

transcriptional regulator NarP; Provisional

false

true

false

215

8e-09

57.18

32.56

2,442,141,12,455,153,58

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41409450 443 QPVGPRPNPRPDgLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQH 513
PRK10403    142 EMFGAEEDPFSV-LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211

-1

138058

PRK10651

transcriptional regulator NarL; Provisional

false

true

false

216

1e-08

56.61

32.87

2,447,142,6,453,153,60

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41409450 448 RPNPRP-----DGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQH 513
PRK10651    143 RANRATterdvNQLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQE 213

-1

132065

TIGR03020

EpsA

transcriptional regulator EpsA

false

true

false

247

1e-08

56.33

29.96

2,436,173,16,454,189,58

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41409450 437 VLHAAGQPVGPRPNPRpdGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQ 512
TIGR03020   174 PNQHRTRPLGERHSAG--LITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAIA 247

-1

137688

PRK10100

DNA-binding transcriptional regulator CsgD; Provisional

false

true

false

216

4e-08

54.57

26.85

1,455,155,58

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 41409450 456 LTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQH 513
PRK10100    156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213

-1

137598

PRK09935

transcriptional regulator FimZ; Provisional

false

true

false

210

4e-07

51.43

29.05

1,455,149,61

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41409450 456 LTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQHGLV 516
PRK09935    150 LSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHELL 210

-1

32388

COG2206

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

true

false

344

3e-06

48.60

29.65

4,133,207,6,139,214,56,195,272,6,201,282,27

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41409450 134 RLIHSH-CASAALLADRIGLGPNVQAALAYTFERYDGGGLPTGARGEDIPIQMRIAQLADMVE--VHHRSY----GVAGA 206
COG2206     208 EIIKKHpIYGYDILKDLPEFLESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDalTSDRPYkkakSPEEA 287

                        90       100
                ....*....|....*....|..
gi 41409450 207 VAMVGARRGGQFDPGIADVFLR 228
COG2206     288 LEELRKNSGGKFDPKVVDAFLK 309

-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

6e-06

47.60

21.67

3,164,276,31,195,309,22,217,335,19

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41409450 165 ERYDGGGLPTGARGEDIPIQMRIAQLADMVE--VHHRSYGVAGAVAMVGARRGGQ----FDPGIADVFLRDADAILAG 236
COG3437     277 ERWDGSGYPDGLKGDEIPLSARIVAIADVFDalVSGRPYKEAMSTEEALEIIRAQsgrlFDPKLVEAFIQVEDEIIDI 354

-1

34204

COG4566

TtrR

Response regulator [Signal transduction mechanisms]

false

true

false

202

2e-05

46.00

25.25

1,451,138,51

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 41409450 452 RPDGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSN 502
COG4566     139 RLATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189

-1

135188

PRK04841

transcriptional regulator MalT; Provisional

false

true

false

903

2e-05

45.75

6.09

1,455,838,55

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 41409450 456 LTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYA 510
PRK04841    839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQLA 893

-1

132580

TIGR03541

reg_near_HchA

LuxR family transcriptional regulatory, chaperone HchA-associated

false

true

false

232

2e-04

42.85

25.43

1,455,171,59

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 41409450 456 LTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQHG 514
TIGR03541   172 LSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKG 230

-1

139792

PRK13719

conjugal transfer transcriptional regulator TraJ; Provisional

false

true

false

220

7e-04

40.89

20.00

1,459,149,44

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 41409450 460 EIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNR 503
PRK13719    150 QYDVFILYSFGFSHNSIASLLNITNGSSKNKISEILKFFGISSR 193

-1

137846

PRK10360

DNA-binding transcriptional activator UhpA; Provisional

false

true

false

196

0.002

39.24

27.04

1,451,133,53

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 41409450 452 RPDGLTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRI 504
PRK10360    134 RQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDV 186

-1

136118

PRK06930

positive control sigma-like factor; Validated

false

true

false

170

0.004

38.16

32.35

3,455,114,8,463,123,36,501,159,10

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 41409450 456 LTPREIEV-LGHVARGASNKEIAAALVISEKTARNHVERTYAKIGvsNRIGASMYAL 511
PRK06930    115 LTEREKEVyLMHRGYGLSYSEIAAYLNIKKSTVQSMIERAEKKIA--KQINESLFCM 169

-1

137737

PRK10188

DNA-binding transcriptional activator SdiA; Provisional

false

true

false

240

0.007

37.49

25.42

1,455,179,61

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41409450 456 LTPREIEVLGHVARGASNKEIAAALVISEKTARNHVERTYAKIGVSNRIGASMYALQHGLV 516
PRK10188    180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240

-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