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Conserved domains on [gi\|117928958\|ref\|YP_873509.1\|]
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

109717

pfam00672

HAMP

HAMP domain

true

false

8e-04

40.67

74.29

1,229,18,52

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 117928958 230 IGRRLRSDINAVASVAEALAEGDLTRQSGVDRSDGLGRLARALDRAVTTLRQ 281
pfam00672     19 LARRLLRPLRRLAEAARRIASGDLDDRVPVSGPDEIGELARAFNQMADRLRE 70

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

128599

smart00304

HAMP

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

false

0.004

38.39

94.34

1,231,0,50

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 117928958 232 RRLRSDINAVASVAEALAEGDLTRQSGVDRSDGLGRLARALDRAVTTLRQ 281
smart00304     1 RRILRPLRRLAEAAQRIADGDLTVRLPVDGRDEIGELARAFNEMADRLEE 50

cl01054

141075

HAMP

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

-1

29143

cd00181

TarH

Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein.

Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar...

true

false

140

0.005

38.07

45.00

2,382,3,43,425,49,17

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 117928958 383 QIGQVVKVITAIAQQTNLLALNATIEAARAGEAGKGFAVVAGE---VKDLAQETARATEDIAR 442
cd00181        4 VILSILRQQQAELDLTRVLLLQARINLNRAGERGMMDQNKIGEkakMALLAYASESLTQAIVH 66

cl00144

140469

TarH

Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar...

128579

smart00283

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

true

false

262

1e-34

143.19

87.40

4,331,33,34,365,74,92,457,168,17,474,190,72

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 332 VQAVSTGGQQMGSSIREISVNASEATRVAGQAVA-------VAQSTNDMVTRLGESSSQIGQVVKVITAIAQQTNLLALN 404
smart00283    34 IEEVAANADEIAATAQSAAEAAEEGREAVEDAITamdqireVVEEAVSAVEELEESSDEIGEIVSVIDDIADQTNLLALN 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 405 ATIEAARAGEAGKGFAVVAGEVKDLAQETARATEDIARRVEAIQADTAGAVAA--ISEISSIIERINEIQTV-----IAS 477
smart00283   114 AAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEAVAAmeESSSEVEEGVELVEETGealeeIVD 193

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 117928958 478 AVEEQTATTNEMNRAVDEAATGAHEIANRIGQVAQAAQQTAGTVANTRHAAEELSRLSGELQQLVGRFR 546
smart00283   194 SVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEISAAAEELSGLAEELKELVEQFK 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

6e-34

140.50

80.39

3,229,79,135,364,218,93,457,318,89

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 230 IGRRLRSDINAVASVAEALAEGDLTRQSGVDRSDGLGRLARALDRAVTTLRQDVASVSAHARTLGSASVQLNSLAAALGT 309
COG0840       80 LLRAILEPISDLLEVVERIAAGDLTKRIDESSNDEFGQLAKSFNEMILNLRQIIDAVQDNAEALSGASEEIAASATELSA 159

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 310 SAEAVSAQATASAEAANAVTNHVQAVSTGGQQMGSSIREISVNASEATRVAGQAV----AVAQSTNDMVTRLGESSSQIG 385
COG0840      160 RADQQAESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVeqmqEIAEELAEVVKKLSESSQEIE 239

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 386 QVVKVITAIAQQTNLLALNATIEAARAGEAGKGFAVVAGEVKDLAQETARATEDIARRVEAIQADTAGAVAA-------I 458
COG0840      240 EITSVINSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIEEIQNEAADAVEHmeesaseV 319

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 459 SEISSIIERINEIQTVIASAVEEQTATTNEMNRAVDEAATGAHEIANRIGQVAQAAQQTAGTVANTRHAAEELSRLSGEL 538
COG0840      320 SEGVKLVEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAEKL 399


                 ....*...
gi 117928958 539 QQLVGRFR 546
COG0840      400 LELVAKFK 407

-1

109084

pfam00015

MCPsignal

Methyl-accepting chemotaxis protein (MCP) signaling domain

false

true

false

241

1e-29

126.38

96.68

4,331,6,33,364,47,15,379,65,93,472,165,74

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 332 VQAVSTGGQQMGSSIREISVNASEATRVAGQAV--------AVAQSTNDMVTRLGE---SSSQIGQVVKVITAIAQQTNL 400
pfam00015      7 IEQVAASMEQLTATVRDIASNAAQASDLAKQASeealeemsQIGQEVDNAVQVMEElatSSKNISDIISVIDEIAFQTNL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 401 LALNATIEAARAGEAGKGFAVVAGEVKDLAQETARATEDIARRVEAIQADTAGAVAAISEISSIIERINEIQ-------T 473
pfam00015     87 LALNAAIEAARAGEQGRGFAVVADEVRKLAERSAQAAKEIEQLIEEIQKESNDAVESMQQTRTQVEVGSTIVektgealK 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 117928958 474 VIASAVEEQTATTNEMNRAVDEAATGAHEIANRIGQVAQAAQQTAGTVANTRHAAEELSRLSGELQQLVGRFR 546
pfam00015    167 EIVEAIGEIADEVQEIAAASEEQSAGIEQINQAVERIDQVTQQNAALVEESSAASESLSEQAEELTALVAQFK 239

-1

137524

PRK09793

methyl-accepting protein IV; Provisional

false

true

false

533

6e-17

84.36

38.84

3,339,305,40,379,352,67,453,419,93

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 340 QQMGSSIREISVNASEATRVAGQAVAVAQSTNDMVTRLGE-------SSSQIGQVVKVITAIAQQTNLLALNATIEAARA 412
PRK09793     306 EQLTATVGQNADNARQASELAKNAATTAQAGGVQVSTMTHtmqeiatSSQKIGDIISVIDGIAFQTNILALNAAVEAARA 385

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928958 413 GEAGKGFAVVAGEVKDLAQETARATEDIARRVEAiqadtagAVAAISEISSIIERINEIQTVIASAVEEQTATTNEMNRA 492
PRK09793     386 GEQGRGFAVVAGEVRNLASRSAQAAKEIKGLIEE-------SVNRVQQGSKLVNNAAATMTDIVSSVTRVNDIMGEIASA 458

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 117928958 493 VDEAATGAHEIANRIGQVAQAAQQTAGTVANTRHAAEELSRLSGELQQLVGRFR 546
PRK09793     459 SEEQRRGIEQVAQAVSQMDQVTQQNASLVEEAAVATEQLANQADHLSSRVAVFT 512

-1

ligand (aspartate) binding pocket	0	4	10	false	29143	cd00181	TarH
dimerization interface	1	14	16	false	29143	cd00181	TarH