NCBI Conserved Domain Search

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Conserved domains on [gi\|117927337\|ref\|YP_871888.1\|]
methyl-accepting chemotaxis sensory transducer [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

128599

smart00304

HAMP

HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain

true

false

7e-04

40.31

75.47

2,85,5,22,108,27,18

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 117927337  86 PMRRAIDVLREAAAGNLTRRLPgVRRRDEFGAMARALNTML 126
smart00304     6 PLRRLAEAAQRIADGDLTVRLP-VDGRDEIGELARAFNEMA 45

cl01054

141075

HAMP

Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.

Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain...

-1

100122

cd06225

HAMP

Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain...

false

0.001

39.54

83.33

2,85,3,22,108,25,18

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 117927337  86 PMRRAIDVLREAAAGNLTRRLPgVRRRDEFGAMARALNTML 126
cd06225        4 PLRRLAEAAQRIAAGDLDVRLP-VTGRDEIGELARAFNQMA 43

cl01054

141075

HAMP

Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain...

-1

128579

smart00283

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

true

false

262

3e-09

58.07

52.29

2,225,84,84,309,189,32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117927337 226 KLGESSAEIGNILKVITSIARQTHLLALNATIEAARAGEAGRGFAVVAAEVKDLADATARATDDIAQMIKTIQDDAAEAV 305
smart00283    85 ELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEAV 164

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 117927337 306 TMIR---------------------QISAVVDRINDFQSTIAGAVEEQTASSNEMTR 341
smart00283   165 AAMEessseveegvelveetgealeEIVDSVEEIADLVQEIAAATDEQAAGSEEVNA 221

-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

3e-08

54.99

63.24

3,85,86,22,108,108,117,225,229,115

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117927337  86 PMRRAIDVLREAAAGNLTRRLPgVRRRDEFGAMARALNTMLDAAADAFFAVTTGIRLLAQTSGRLAQTATKLADSADRAS 165
COG0840       87 PISDLLEVVERIAAGDLTKRID-ESSNDEFGQLAKSFNEMILNLRQIIDAVQDNAEALSGASEEIAASATELSARADQQA 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117927337 166 DQSTLVSYAADQVSSNVVGVAGSSEQMAAAIRDIADNASRAAAVAAEAAATAERADSTVA----KLGESSAEIGNILKVI 241
COG0840      166 ESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQMQEIAEELAevvkKLSESSQEIEEITSVI 245

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117927337 242 TSIARQTHLLALNATIEAARAGEAGRGFAVVAAEVKDLADATARATDDIAQMIKTIQDDAAEAVTMIRQISAVVDRINDF 321
COG0840      246 NSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIEEIQNEAADAVEHMEESASEVSEGVKL 325

                        250
                 ....*....|....*....
gi 117927337 322 QSTIAGAVEEQTASSNEMT 340
COG0840      326 VEETGSSLGEIAAAIEEVS 344

-1

109084

pfam00015

MCPsignal

Methyl-accepting chemotaxis protein (MCP) signaling domain

false

true

false

241

2e-05

45.49

56.43

2,226,62,84,310,167,31

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117927337 227 LGESSAEIGNILKVITSIARQTHLLALNATIEAARAGEAGRGFAVVAAEVKDLADATARATDDIAQMIKTIQDDAAEAVT 306
pfam00015     63 LATSSKNISDIISVIDEIAFQTNLLALNAAIEAARAGEQGRGFAVVADEVRKLAERSAQAAKEIEQLIEEIQKESNDAVE 142

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 117927337 307 MIRQ---------------------ISAVVDRINDFQSTIAGAVEEQTASSNEMTR 341
pfam00015    143 SMQQtrtqvevgstivektgealkeIVEAIGEIADEVQEIAAASEEQSAGIEQINQ 198

-1