NCBI Conserved Domain Search

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Conserved domains on [gi\|117928173\|ref\|YP_872724.1\|]
response regulator receiver protein [Acidothermus cellulolyticus 11B]

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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

29071

cd00156

REC

Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC,...

true

false

113

2e-04

39.84

96.46

4,17,4,16,39,20,44,84,64,20,104,86,27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928173  18 DDATVRERVRLALGRRpapdlpELRYIECATQYAVLEAADHENVDLFILDGEAVPAGGMGLCRQLKdEIYRCPPVIVLIA 97
cd00156        5 DDPLIRELLRRLLEKE------GYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELLRRIR-KRGPDIPIIFLTA 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 117928173  98 RRDDGWL--ATWSRADATVLHPVDGVRLTPVVVDLL 131
cd00156       78 HGDDEDAveALKAGADDYLTKPFSPEELLARIRALL 113

cl09944

142340

REC

Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC,...

31088

COG0745

OmpR

Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]

Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-...

false

true

false

229

0.002

36.47

35.81

3,12,2,21,39,23,18,58,41,43

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928173  13 VVVYSDDATVRERVRLALGRRpapdlpELRYIECATQYAVLEAADhENVDLFILDGEAVPAGGMGLCRQLKDEIYRCPPV 92
COG0745        3 ILLVEDDPELAELLKEYLEEE------GYEVDVAADGEEALEAAR-EQPDLVLLDLMLPDLDGLELCRRLRAKKGSGPPI 75


                 ....*....
gi 117928173  93 IVLIARRDD 101
COG0745       76 IVLTARDDE 84

-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

0.006

34.89

36.67

5,0,4,30,31,34,16,52,50,31,83,83,17,100,102,34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928173   1 MPHTAHRVETRTVVVYSDDATVRERVRLALgRRPAPDLPELRYIECAtqyavLEAADHENVDLFILDGEAVPAGGMGLCR 80
COG3437        5 MQGKNEPDEKLTVLLVDDEPDNLEALRQLL-RMIGYRVIEAENGEEA-----LKLLQEEPPDLVLLDVRMPEMDGAEVLN 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117928173  81 QLK--DEIYRCPPVIVLIARRD--DGWLATWSRADATVLHPVDGVRLTPVVVDLLRRR 134
COG3437       79 KLKamSPSTRRIPVILLTAYADseDRQRALEAGADDYLSKPISPKELVARVSSHLQLK 136

-1

active site	0	7	8	false	29071	cd00156	REC
phosphorylation site	1	1	1	false	29071	cd00156	REC
intermolecular recognition site	2	5	5	false	29071	cd00156	REC
dimerization interface	3	3	3	false	29071	cd00156	REC