NCBI Conserved Domain Search

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Conserved domains on [gi\|94968699\|ref\|YP_590747.1\|]
methyl-accepting chemotaxis sensory transducer [Candidatus Koribacter versatilis Ellin345]

Graphical summary show options »	Show site features Horizontal zoom: ×	?



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

2e-09

59.93

100.00

1,192,0,70

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 193 IVGFMVFGVFAAIALGWFLTRLIVGPVRELQATATKLAAGDVEVDIKANTNDELGKLAQSIAALAATIKD 262
pfam00672     1 LLLVLLIALLLLLLLAWLLARRLLRPLRRLAEAARRIASGDLDDRVPVSGPDEIGELARAFNQMADRLRE 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

6e-05

45.32

100.00

1,212,0,53

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 94968699 213 RLIVGPVRELQATATKLAAGDVEVDIKANTNDELGKLAQSIAALAATIKDRAQ 265
smart00304    1 RRILRPLRRLAEAAQRIADGDLTVRLPVDGRDEIGELARAFNEMADRLEETIA 53

cl01054

141075

HAMP

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

1e-04

43.78

100.00

1,214,0,48

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 94968699 215 IVGPVRELQATATKLAAGDVEVDIKANTNDELGKLAQSIAALAATIKD 262
cd06225       1 ILRPLRRLAEAAQRIAAGDLDVRLPVTGRDEIGELARAFNQMAERLRE 48

cl01054

141075

HAMP

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

-1

32631

COG2770

ResE

FOG: HAMP domain [Signal transduction mechanisms]

false

0.003

39.23

85.54

2,187,1,19,206,21,51

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 94968699 188 SATQQIVGFMVFGVFAAIA-LGWFLTRLIVGPVRELQATATKLAAGDVEVDIKANTNDELGKLAQSIAALA 257
COG2770       2 HSTAPIFGLLVLALVLILAvLLLAAARRVTRPLRRLADLAQNLALGDLSAEIPQPMLDEIGELAKAFNRMR 72

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-45

179.02

98.85

3,626,3,176,802,180,4,806,190,72

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 627 EAATMLNNVSQQMTASADETATQANVVSAASEQVSRNVQTVASGADQMGASIKEIAKNTAEATRVANSAVQTAEATNQNI 706
smart00283    4 EAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAV 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 707 GKLGQSSAEIGQVIKVITSIAQQTNLLALNATIEAARAGEAGKGFAVVANEVKELAKETAKATEDIGRKIEAIQTDTTGA 786
smart00283   84 EELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEA 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 787 VSAIAEIGAVINQISD-IQTT------IASAVEEQSVTSNEISRNLAEAAKGNVDITRNVTGVAEAARVTTTGAAETQKS 859
smart00283  164 VAAMEESSSEVEEGVElVEETgealeeIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEISAA 243

                       250
                ....*....|....*....
gi 94968699 860 AKSLERMAVELKKLVSRFK 878
smart00283  244 AEELSGLAEELKELVEQFK 262

-1

109084

pfam00015

MCPsignal

Methyl-accepting chemotaxis protein (MCP) signaling domain

false

true

false

241

3e-34

142.56

99.17

3,657,0,51,708,62,96,804,165,74

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 658 EQVSRNVQTVASGADQMGASIKEIAKNTAEATRVANSAVQTAEATNQNIGK-----------LGQSSAEIGQVIKVITSI 726
pfam00015     1 EEQASAIEQVAASMEQLTATVRDIASNAAQASDLAKQASEEALEEMSQIGQevdnavqvmeeLATSSKNISDIISVIDEI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 727 AQQTNLLALNATIEAARAGEAGKGFAVVANEVKELAKETAKATEDIGRKIEAIQTDTTGAVSAIAEIGAVINQISDIQ-- 804
pfam00015    81 AFQTNLLALNAAIEAARAGEQGRGFAVVADEVRKLAERSAQAAKEIEQLIEEIQKESNDAVESMQQTRTQVEVGSTIVek 160

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 94968699 805 -----TTIASAVEEQSVTSNEISRNLAEAAKGNVDITRNVTGVAEAARVTTTGAAETQKSAKSLERMAVELKKLVSRFK 878
pfam00015   161 tgealKEIVEAIGEIADEVQEIAAASEEQSAGIEQINQAVERIDQVTQQNAALVEESSAASESLSEQAEELTALVAQFK 239

-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-30

130.10

78.92

4,559,85,29,596,114,102,698,220,98,796,325,82

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 560 RQAQKLSDALKELAQGNLNALMVTDASDAdtdearktYEVISDAFAKSAAAFRGAMMDIGRTTEALLEAATMLNNVSQQM 639
COG0840      86 EPISDLLEVVERIAAGDLTKRIDESSNDE--------FGQLAKSFNEMILNLRQIIDAVQDNAEALSGASEEIAASATEL 157

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 640 TASADETATQANVVSAASEQVSRNVQTVASGADQMGASIKEIAKNTAEATRVANSAVQT----AEATNQNIGKLGQSSAE 715
COG0840     158 SARADQQAESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQmqeiAEELAEVVKKLSESSQE 237

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 716 IGQVIKVITSIAQQTNLLALNATIEAARAGEAGKGFAVVANEVKELAKETAKATEDIGRKIEAIQTDTTGAVSAIAEIGA 795
COG0840     238 IEEITSVINSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIEEIQNEAADAVEHMEESAS 317

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 796 V-------INQISDIQTTIASAVEEQSVTSNEISRNLAEAAKGNVDITRNVTGVAEAARVTTTGAAETQKSAKSLERMAV 868
COG0840     318 EvsegvklVEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAE 397

                       330
                ....*....|
gi 94968699 869 ELKKLVSRFK 878
COG0840     398 KLLELVAKFK 407

-1

137524

PRK09793

methyl-accepting protein IV; Provisional

false

true

false

533

6e-23

104.77

51.97

7,622,256,89,711,352,67,778,423,5,783,431,31,821,462,9,840,471,38,878,510,23

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 623 EALLEAATMLNNVSQQMTASADETATQANVVSAASEQVSRNVQTVASGADQMGASIKEIAKNTAEATRVANSAVQTAEAT 702
PRK09793    257 QALRGTVSDVRKGSQEMHIGIAEIVAGNNDLSSRTEQQAASLAQTAASMEQLTATVGQNADNARQASELAKNAATTAQAG 336

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 703 NQNIGKLGQ-------SSAEIGQVIKVITSIAQQTNLLALNATIEAARAGEAGKGFAVVANEVKELAKETAKATEDIGRK 775
PRK09793    337 GVQVSTMTHtmqeiatSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLASRSAQAAKEIKGL 416

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 776 IEA----IQTDT---TGAVSAIAEIGAVINQISDIQTTIASAVEEQsvtsneiSRNLAEAAKgnvditrnvtGVAEAARV 848
PRK09793    417 IEEsvnrVQQGSklvNNAAATMTDIVSSVTRVNDIMGEIASASEEQ-------RRGIEQVAQ----------AVSQMDQV 479

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 94968699 849 TTTGAAETQKSAKSLERMAVELKKLVSRFK-YDGEQNSRSLAVSSRADRMPATS 901
PRK09793    480 TQQNASLVEEAAVATEQLANQADHLSSRVAvFTLEEHEVARHESAQLQIAPVVS 533

-1

117025

pfam08448

PAS_4

PAS fold

true

false

110

4e-07

52.42

100.00

3,438,0,72,510,74,30,545,104,6

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 439 FDAIPKPIQFIDSQFKVQYMNKAGLELMGKSAESAIGSRCSYNTSACGTEKCTCAQAMKIDGLTRIETQARI--QGKQYD 516
pfam08448     1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRALEGEEPIDFLEELllNGEERH 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 94968699 517 FTCCAVPLKDGNGRTIGAFELMDDeslikTTMRKA 551
pfam08448    81 YELRLTPLRDPDGEVIGVLVISRD-----ITERRR 110

-1

137977

PRK10549

signal transduction histidine-protein kinase BaeS; Provisional

false

true

false

467

1e-06

50.88

14.99

3,192,169,6,200,175,7,208,182,57

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 94968699 193 IVGFMVfgVFAAIALgWFLTRLIVGPVRELQATATKLAAGDVEVDIKANTNDELGKLAQSIAALAATIKDRAQ 265
PRK10549    170 IVALST--LLAALAT-FLLARGLLAPVKRLVEGTHKLAAGDFTTRVTPTSEDELGKLAQDFNQLASTLEKNQQ 239

-1

132001

TIGR02956

TMAO_torS

TMAO reductase sytem sensor TorS

false

true

false

968

3e-04

42.46

11.88

3,194,331,25,219,358,7,226,367,79

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 195 GFMVFGVFAAIALGWFLTRLIVGPV--RELQATA--TKLAAGDVEVDIKANTNDELGKLAQSIAALAATIKDRAQAAQHI 270
TIGR02956   332 GLLITGMLGLVILVFIMWRVVYRSVilRLNQHTQalLRLALGDLDISLDARGDDELAHMGRAIEAFRDTAAHNLKLQADE 411

                        90       100       110
                ....*....|....*....|....*....|....*
gi 94968699 271 AQGDLQLQIKPASDKDVLAKSLQSLVDTLNGLMQE 305
TIGR02956   412 RQVAQELQEHKESLEQLVAQRTQELAETNERLNAE 446

-1

31700

COG1511

Predicted membrane protein [Function unknown]

false

true

false

780

8e-04

41.23

30.51

1,624,203,238

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 625 LLEAATMLNNVSQQMTASADETATQANVVSAASEQVSRNVQTVASGADQMGASIKEIAKNTAEATRVANSAVQTAEATNQ 704
COG1511     204 LSDLLNTLNNSSATFSDGLNALTSGLTTLTDGLNQLDSGLGTLAAGIGELKQGAEQLNEGIGEFSSGLSELNSGVQDLAA 283

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968699 705 NIGKLGQSSAEIGQVIKVITSIAQQTNLLALNATIEAARAGEAGKGFAVVANEVKELAKETAKATEDIGRKIEAIQTDTT 784
COG1511     284 GVPQLNQGISALAAGLSLPDSLGDQFSSLQEALTQIAQGLKQKTSSSLEAAQGSLSSLQSMLALSKSLDLTAEGATVDAL 363

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 94968699 785 GAVSAIAEIGAVINQISDIQTTIASAVEEQSVTSNEISRNLAEAAKGNVDITRNVTGVAEAARVTTTGAAETQKSAKS 862
COG1511     364 GAPDGVQWLDESQKTLATLSELLSTGIDGVSEGLDALEQASAQLAKSLAKLKTAVAQIAASIAQLLPGASEVLKTLKS 441

-1

34605

COG5000

NtrY

Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]

Signal transduction histidine kinase involved in nitrogen fixation and metabolism...

false

true

false

712

0.001

40.71

9.41

2,176,268,22,200,290,45

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 94968699 177 KREKENSALAASATQQIVGFMVfgVFAAIALGWFLTRLIVGPVRELQATATKLAAGDVEVDIKANTNDE 245
COG5000     269 EAGRDGLQIAFALLYLSTALLV--LLAAIWTAIAFARRIVRPIRKLIEAADEVADGDLDVQVPVRRVDE 335

-1