NCBI Conserved Domain Search

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Conserved domains on [gi\|94968554\|ref\|YP_590602.1\|]
methyl-accepting chemotaxis sensory transducer [Candidatus Koribacter versatilis Ellin345]

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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

128579

smart00283

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

true

false

262

4e-34

142.04

98.85

2,581,3,179,760,189,73

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 582 QSSDELSRISREMEATSEQTSAQANMASAGSEQVSKNVQTVATGADEMGASIREIAKSTGEASKVATAAVQTADHTNATI 661
smart00283    4 EAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAV 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 662 AKLGQSSAEIGEVIKVITSIAQQTNLLALNATIEAARAGDAGKGFAVVANEVKELAKETAKATEDISQKIVAIQGDTKGA 741
smart00283   84 EELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEA 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 742 VGAIGEIGAVIGQINDIQH-------GIASAVEEQSATTSEISRNLAEAARGAVDITANVTAVASAARAATQGATETGKS 814
smart00283  164 VAAMEESSSEVEEGVELVEetgealeEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEISAA 243

                       250
                ....*....|....*....
gi 94968554 815 AQALQKMAVDLDAMIARFK 833
smart00283  244 AEELSGLAEELKELVEQFK 262

-1

109084

pfam00015

MCPsignal

Methyl-accepting chemotaxis protein (MCP) signaling domain

false

true

false

241

1e-26

117.14

99.59

3,612,0,51,663,62,96,759,165,75

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 613 EQVSKNVQTVATGADEMGASIREIAKSTGEASKVATAAVQTADHTNATIAK-----------LGQSSAEIGEVIKVITSI 681
pfam00015     1 EEQASAIEQVAASMEQLTATVRDIASNAAQASDLAKQASEEALEEMSQIGQevdnavqvmeeLATSSKNISDIISVIDEI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 682 AQQTNLLALNATIEAARAGDAGKGFAVVANEVKELAKETAKATEDISQKIVAIQGDTKGAVGAIGEIGAVIGQINDIQ-- 759
pfam00015    81 AFQTNLLALNAAIEAARAGEQGRGFAVVADEVRKLAERSAQAAKEIEQLIEEIQKESNDAVESMQQTRTQVEVGSTIVek 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 760 -----HGIASAVEEQSATTSEISRNLAEAARGAVDITANVTAVASAARAATQGATETGKSAQALQKMAVDLDAMIARFKL 834
pfam00015   161 tgealKEIVEAIGEIADEVQEIAAASEEQSAGIEQINQAVERIDQVTQQNAALVEESSAASESLSEQAEELTALVAQFKL 240

-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

1e-24

110.46

80.64

4,515,79,32,548,111,105,653,220,86,739,313,95

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 516 MKENILALQQEMNGIIQAADRGDLTYRADEAAlHGAYAELLAGMNRVLEIVRSTMLQISKIAAPLKQSSDELSRISREME 595
COG0840      80 LLRAILEPISDLLEVVERIAAGDLTKRIDESS-NDEFGQLAKSFNEMILNLRQIIDAVQDNAEALSGASEEIAASATELS 158

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 596 ATSEQTSAQANMASAGSEQVSKNVQTVATGADEMGASIREIAKSTGEASKVATAAVQT----ADHTNATIAKLGQSSAEI 671
COG0840     159 ARADQQAESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQmqeiAEELAEVVKKLSESSQEI 238

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 672 GEVIKVITSIAQQTNLLALNATIEAARAGDAGKGFAVVANEVKELAKETAKATEDISQKIVAIQGDTK-------GAVGA 744
COG0840     239 EEITSVINSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIEEIQNEAAdavehmeESASE 318

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 745 IGEIGAVIGQINDIQHGIASAVEEQSATTSEISRNLAEAARGAVDITANVTAVASAARAATQGATETGKSAQALQKMAVD 824
COG0840     319 VSEGVKLVEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAEK 398

                       330
                ....*....|
gi 94968554 825 LDAMIARFKL 834
COG0840     399 LLELVAKFKL 408

-1

137524

PRK09793

methyl-accepting protein IV; Provisional

false

true

false

533

4e-19

92.06

40.71

4,579,258,75,654,340,72,726,416,13,739,432,43

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 580 LKQSSDELSRISREMEATSEQTSAQANMASAGSEQVSKNVQTVATGADEMGASIREIAKSTGEASKVATAAVQTA----- 654
PRK09793    259 LRGTVSDVRKGSQEMHIGIAEIVAGNNDLSSRTEQQAASLAQTAASMEQLTATVGQNADNARQASELAKNAATTAqaggv 338

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968554 655 --DHTNATIAKLGQSSAEIGEVIKVITSIAQQTNLLALNATIEAARAGDAGKGFAVVANEVKELAKETAKATED----IS 728
PRK09793    339 qvSTMTHTMQEIATSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLASRSAQAAKEikglIE 418

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 94968554 729 QKIVAIQGDTK---GAVGAIGEIGAVIGQINDIQHGIASAVEEQSATTSEISRNLAE 782
PRK09793    419 ESVNRVQQGSKlvnNAAATMTDIVSSVTRVNDIMGEIASASEEQRRGIEQVAQAVSQ 475

-1