NCBI Conserved Domain Search

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Conserved domains on [gi\|116620196\|ref\|YP_822352.1\|]
methyl-accepting chemotaxis sensory transducer [Solibacter usitatus Ellin6076]

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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

34875

COG5278

Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]

true

false

207

3e-04

42.21

99.52

8,0,0,42,43,42,30,79,72,8,88,80,39,129,119,10,139,132,19,158,152,35,193,188,18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196   1 MNSQMTIGKKLMLSFAGLIVLLVTLSFTFLSVVGTLKGTFDEaVDKTARKLSLAGDLDAAESDMLAWQRGMLLyalskdT 80
COG5278        1 MTKRMPIRKKIILSFVIGVLLLLLASGASYWSIQKSNQSTRE-VIETQQVLAAALDLLSAVSDAESGQRGYLL------T 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196  81 AKSEAARgRFRKSLESANQALTEITPLLVNEEGRKLTASTKAGLNAWanHFAESDRLCA---AGDPSAGFQYAATNTVSI 157
COG5278       74 GNDEYLE-PYEEATEELDQKLEELRALTADDPELLESLDDLEPLIQW--KLAEADETIPlrrDGKLEAAVQIISSDQGKV 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 116620196 158 F-EELTGQVTRLKEIQNARLQENRAEASAENISSRWI-AFVMLALSLGLGAIVFLV 211
COG5278      151 LmDAIRQYLQEIEEEENERLTQALAEQQNAARTLRIAlIIGGIVILLVAVMLALAL 206

cl05000

123601

CHASE3

CHASE3 domain

-1

137524

PRK09793

methyl-accepting protein IV; Provisional

true

false

533

3e-17

85.13

37.34

1,273,313,199

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 274 RNTENSNSAAALVAQSQRQFEDTRTSLNAMVTAMTDITTSSGKISKIIKVIDEIAFQTNILALNAAVEAARAGEAGLGFA 353
PRK09793     314 QNADNARQASELAKNAATTAQAGGVQVSTMTHTMQEIATSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGFA 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 354 VVADEVRNLAQRCAQAAKDTADLIEDSVAKSNAGKAKVDQVADAIRMVTEEAGKIKVLVDEISVGSQEQARGIEQIGSAI 433
PRK09793     394 VVAGEVRNLASRSAQAAKEIKGLIEESVNRVQQGSKLVNNAAATMTDIVSSVTRVNDIMGEIASASEEQRRGIEQVAQAV 473

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 116620196 434 TQMDQVTQRAAASAEEGASAAEELTAQSESLKAVVGELT 472
PRK09793     474 SQMDQVTQQNASLVEEAAVATEQLANQADHLSSRVAVFT 512

-1

109084

pfam00015

MCPsignal

Methyl-accepting chemotaxis protein (MCP) signaling domain

false

true

false

241

3e-17

85.17

89.63

4,272,21,17,289,42,97,386,153,55,448,208,29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 273 RRNTENSNSAAALVAQS----QRQFEDTRTSLNAMVTAMTDITTSSGKISKIIKVIDEIAFQTNILALNAAVEAARAGEA 348
pfam00015     22 RDIASNAAQASDLAKQAseeaLEEMSQIGQEVDNAVQVMEELATSSKNISDIISVIDEIAFQTNLLALNAAIEAARAGEQ 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 349 GLGFAVVADEVRNLAQRCAQAAKDTADLIEDSVAKSNA--------------GKAKVDQVADAIRMVTEEAGKIKVLVDE 414
pfam00015    102 GRGFAVVADEVRKLAERSAQAAKEIEQLIEEIQKESNDavesmqqtrtqvevGSTIVEKTGEALKEIVEAIGEIADEVQE 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116620196 415 ISVGSQEQARGIEQIGSAITQMDQVTQraaasaeEGASAAEELTAQSESLKAVVGELTRMVGG 477
pfam00015    182 IAAASEEQSAGIEQINQAVERIDQVTQ-------QNAALVEESSAASESLSEQAEELTALVAQ 237

-1

128579

smart00283

Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer).

false

true

false

262

2e-16

82.72

82.82

2,269,45,108,377,167,95

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 270 SMARRNTENSNSAAALVAQSQRQFEDTRTSLNAMVTAMTDITTSSGKISKIIKVIDEIAFQTNILALNAAVEAARAGEAG 349
smart00283    46 ATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAG 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 350 LGFAVVADEVRNLAQRCAQAAKDTADLI--------------EDSVAKSNAGKAKVDQVADAIRMVTEEAGKIKVLVDEI 415
smart00283   126 RGFAVVADEVRKLAERSAESAKEIESLIkeiqeetneavaamEESSSEVEEGVELVEETGEALEEIVDSVEEIADLVQEI 205

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 116620196 416 SVGSQEQARGIEQIGSAITQMDQVTQRAAASAEEGASAAEELTAQSESLKAVVGELT 472
smart00283   206 AAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEISAAAEELSGLAEELKELVEQFK 262

-1

31182

COG0840

Tar

Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]

Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction...

false

true

false

408

5e-07

51.14

39.46

2,324,245,53,377,312,94

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 325 DEIAFQTNILALNAAVEAARAGEAGLGFAVVADEVRNLAQRCAQAAKDTADLI--------------EDSVAKSNAGKAK 390
COG0840      246 NSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIeeiqneaadavehmEESASEVSEGVKL 325

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116620196 391 VDQVADAIRMVTEEAGKIKVLVDEISVGSQEQARGIEQIGSAITQMDQVTQRAAASAEEGASAAEELTAQSESLKAVVGE 470
COG0840      326 VEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAEKLLELVAK 405


                 .
gi 116620196 471 L 471
COG0840      406 F 406

-1