NCBI Conserved Domain Search

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Conserved domains on [gi\|94968801\|ref\|YP_590849.1\|]
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

5e-09

58.39

100.00

2,193,0,39,233,39,31

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 94968801 194 SAFVALIAVLAGLFIARRTAKSIVDPIDALNKMAGEIGEsGDLEHTVEIERDDEVGDLAKTFNSMVTYLTE 264
pfam00672     1 LLLVLLIALLLLLLLAWLLARRLLRPLRRLAEAARRIAS-GDLDDRVPVSGPDEIGELARAFNQMADRLRE 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

34875

COG5278

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

true

false

207

1e-06

49.92

97.58

4,0,0,141,148,141,6,156,147,10,166,159,43

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801   1 MTGRNTIRKRLMISFGAIIALVVVLFIASFLSVMRERSAKAAAQTAIDMQSAIEKLRMQMMENRVALAGYVLTGGPAPLA 80
COG5278       1 MTKRMPIRKKIILSFVIGVLLLLLASGASYWSIQKSNQSTREVIETQQVLAAALDLLSAVSDAESGQRGYLLTGNDEYLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801  81 KFNSGVEEFDHLLSDARSKAYSEGQRTALKELEDRNRNWKEKFALPLIQVGKSVEMGNATAtdvqlkyITVSNEwaGQPQ 160
COG5278      81 PYEEATEELDQKLEELRALTADDPELLESLDDLEPLIQWKLAEADETIPLRRDGKLEAAVQ-------IISSDQ--GKVL 151

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 94968801 161 PDEALD--NAERDNAQELTQRRERDSTSSLVTLVASAFVALIAVLAGLFIA 209
COG5278     152 MDAIRQylQEIEEEENERLTQALAEQQNAARTLRIALIIGGIVILLVAVML 202

cl05000

123601

CHASE3

CHASE3 domain

-1

100122

cd06225

HAMP

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

false

6e-05

44.55

100.00

2,215,0,16,232,16,32

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 94968801 216 IVDPIDALNKMAGEIGeSGDLEHTVEIERDDEVGDLAKTFNSMVTYLTE 264
cd06225       1 ILRPLRRLAEAAQRIA-AGDLDVRLPVTGRDEIGELARAFNQMAERLRE 48

cl01054

141075

HAMP

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

2e-04

43.01

100.00

2,213,0,19,233,19,34

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 94968801 214 KSIVDPIDALNKMAGEIGEsGDLEHTVEIERDDEVGDLAKTFNSMVTYLTEMAS 267
smart00304    1 RRILRPLRRLAEAAQRIAD-GDLTVRLPVDGRDEIGELARAFNEMADRLEETIA 53

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

2e-40

162.46

99.24

2,341,0,70,418,70,190

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 342 EVTSTMHEMSVNVQNMVKNTQMQASNVSETSASIDQMVASIQRVADTAKVLLDISNKSREEVHSGITTMTkatdglgRIN 421
smart00283    1 DVSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMD-------QIR 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 422 TAIQSSSDIIDALGQRADDIGKIIEVIDDLAEQTNLLALNAAIEAARAGEHGLGFAVVADEVRKLAEKSAQSTKEISDLI 501
smart00283   74 EVVEEAVSAVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLI 153

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 502 QSIQKEARKAVENMEKSTTIVNEGLMLGNELSVALKKISTVVTEVYKFAQEIGAATNEQSHGSSQIARATTRLNEITHEI 581
smart00283  154 KEIQEETNEAVAAMEESSSEVEEGVELVEETGEALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQET 233

                       250       260
                ....*....|....*....|....*..
gi 94968801 582 NSAVEEQAGGAQQVVRAMERMRELIQQ 608
smart00283  234 AAMSEEISAAAEELSGLAEELKELVEQ 260

-1

109084

pfam00015

MCPsignal

Methyl-accepting chemotaxis protein (MCP) signaling domain

false

true

false

241

8e-33

137.17

97.51

2,363,2,39,412,41,196

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 364 QASNVSETSASIDQMVASIQRVADTAKVLLDISNKSREEvhsgittmtkATDGLGRINTAIQSSSDIIDALGQRADDIGK 443
pfam00015     3 QASAIEQVAASMEQLTATVRDIASNAAQASDLAKQASEE----------ALEEMSQIGQEVDNAVQVMEELATSSKNISD 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 444 IIEVIDDLAEQTNLLALNAAIEAARAGEHGLGFAVVADEVRKLAEKSAQSTKEISDLIQSIQKEARKAVENMEKSTTIVN 523
pfam00015    73 IISVIDEIAFQTNLLALNAAIEAARAGEQGRGFAVVADEVRKLAERSAQAAKEIEQLIEEIQKESNDAVESMQQTRTQVE 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 524 EGLMLGNELSVALKKISTVVTEVYKFAQEIGAATNEQSHGSSQIARATTRLNEITHEINSAVEEQAGGAQQVVRAMERMR 603
pfam00015   153 VGSTIVEKTGEALKEIVEAIGEIADEVQEIAAASEEQSAGIEQINQAVERIDQVTQQNAALVEESSAASESLSEQAEELT 232


                ....*
gi 94968801 604 ELIQQ 608
pfam00015   233 ALVAQ 237

-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-29

124.33

79.41

4,255,81,33,288,116,47,363,163,63,429,226,179

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 256 NSMVTYLTEMASTSEAIAGGDLTVDVRPRSSRD--TLGNAFLGMTEGLRMLVGRVRDSAAQVAAGSNQVADASDESAKIS 333
COG0840      82 RAILEPISDLLEVVERIAAGDLTKRIDESSNDEfgQLAKSFNEMILNLRQIIDAVQDNAEALSGASEEIAASATELSARA 161

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 334 VQassaidevtstmhemsvnvqnmvkntqmQASNVSETSASIDQMVASIQRVADTAKVLLDISNKSREEVHSGITTMTKA 413
COG0840     162 DQ----------------------------QAESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQA 213

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 414 TDGLGRINTAIQSssdIIDALGQRADDIGKIIEVIDDLAEQTNLLALNAAIEAARAGEHGLGFAVVADEVRKLAEKSAQS 493
COG0840     214 VEQMQEIAEELAE---VVKKLSESSQEIEEITSVINSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADS 290

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 494 TKEISDLIQSIQKEARKAVENMEKSTTIVNEGLMLGNELSVALKKISTVVTEVYKFAQEIGAATNEQSHGSSQIARATTR 573
COG0840     291 AKEIGLLIEEIQNEAADAVEHMEESASEVSEGVKLVEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEE 370

                       330       340       350
                ....*....|....*....|....*....|....*
gi 94968801 574 LNEITHEINSAVEEQAGGAQQVVRAMERMRELIQQ 608
COG0840     371 LDDVTQENAAAVEELAAASEELKELAEKLLELVAK 405

-1

137524

PRK09793

methyl-accepting protein IV; Provisional

false

true

false

533

4e-21

98.61

43.15

4,348,278,42,397,320,29,433,349,68,515,417,91

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 349 EMSVNVQNMVKNTQMQASNVSETSASIDQMVASIQRVADTAKvlldisnKSREEVHSGITTMTKATDGLGRINTAIQSss 428
PRK09793    279 EIVAGNNDLSSRTEQQAASLAQTAASMEQLTATVGQNADNAR-------QASELAKNAATTAQAGGVQVSTMTHTMQE-- 349

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 429 diidaLGQRADDIGKIIEVIDDLAEQTNLLALNAAIEAARAGEHGLGFAVVADEVRKLAEKSAQSTKEISDLIqsiqkea 508
PRK09793    350 -----IATSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLASRSAQAAKEIKGLI------- 417

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 509 rkavenmEKSTTIVNEGLMLGNELSVALKKISTVVTEVYKFAQEIGAATNEQSHGSSQIARATTRLNEITHEINSAVEEQ 588
PRK09793    418 -------EESVNRVQQGSKLVNNAAATMTDIVSSVTRVNDIMGEIASASEEQRRGIEQVAQAVSQMDQVTQQNASLVEEA 490

                       250
                ....*....|....*...
gi 94968801 589 AGGAQQVVRAMERMRELI 606
PRK09793    491 AVATEQLANQADHLSSRV 508

-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

4e-07

51.88

19.52

6,156,243,17,173,265,19,195,284,37,233,321,10,243,332,16,262,348,34

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 157 GQPQPDEALDNAERDNA-----QELTQRRERDSTSSLVTLVasaFVALIAVLAGLFIARRTAKSIVDPIDALNKMAGEIG 231
COG5000     244 VRPVDPKVAEHADLTEGaaaeyRELEAGRDGLQIAFALLYL---STALLVLLAAIWTAIAFARRIVRPIRKLIEAADEVA 320

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 94968801 232 EsGDLEHTVEIE-RDDEVGDLAKTFNSMVtylTEMASTSEAIAGGDLTVDVRPRSSRDTLGNAFLG 296
COG5000     321 D-GDLDVQVPVRrVDEDVGRLSKAFNKMT---EQLSSQQEALERAKDALEQRRRFLEAVLSGLTAG 382

-1

138290

PRK10935

nitrate/nitrite sensor protein NarQ; Provisional

false

true

false

568

1e-04

43.71

13.20

3,187,146,17,204,164,26,231,190,31

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 94968801 188 LVTLVASAFVALIAVLA-GLFIARRTAKSIVDPIDALNKMAGEIgESGDLEHTVEIERDDEVGDLAKTFNSMVTYL 262
PRK10935    147 LILLVAISLLGLILILTlVFFTVRFTRRQVVAPLNQLVTASQQI-QKGQFDIPLDTTLPNELGLLAKAFNQMASEL 221

-1

33640

COG3850

NarQ

Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]

Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction...

false

true

false

574

3e-04

42.58

16.38

4,173,135,12,187,147,17,205,164,27,233,191,38

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 174 QELTQRRERDSTssLVTLVASAFVALIAVLAgLFIARRTAKSIVDPIDALNKMAGEIGEsGDLEHTVEIERDDEVGDLAK 253
COG3850     136 LALQRFAERKTI--LLVLVQLAGMLLILLLV-VFTIYWLRRRVVRPLNQLTSAAQRIGR-RQFDQRPTDTGRNELGLLGR 211

                        90
                ....*....|....*...
gi 94968801 254 TFNSMVTYLTEMASTSEA 271
COG3850     212 AFNQMSGELKKLYADLEQ 229

-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-04

41.51

77.70

4,363,89,61,424,151,110,534,268,25,559,328,78

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 364 QASNVSETSASIDQMVASIQRVADTAKVLLDISNKSREEVHSGITTMTKATDGLGRINTAI-QSSSDIIDALGQRADDIG 442
COG0840      90 DLLEVVERIAAGDLTKRIDESSNDEFGQLAKSFNEMILNLRQIIDAVQDNAEALSGASEEIaASATELSARADQQAESLE 169

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 443 KIIEVIDDLAEQTNLLALNAAIEAARAGEHGLGFAVVADEVRKLAEKSAQSTKEISDLIQSIQKEARKAVENMEKSTTIV 522
COG0840     170 EVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQMQEIAEELAEVVKKLSESSQEIEEITSVINSIA 249

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94968801 523 NEGLMLGNELSV-------ALKKISTVVTEVYKFAQEIGAATNE-----------------------------------Q 560
COG0840     250 EQTNLLALNAAIeaarageAGRGFAVVADEVRKLAERSADSAKEigllieeiqneaadavehmeesasevsegvklveeT 329

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 94968801 561 SHGSSQIARATTRLNEITHEINSAVEEQAGGAQQVVRAMERMRELIQQSTSGSTELAASAEQMSKMSRQLLDAMDRF 637
COG0840     330 GSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAEKLLELVAKF 406

-1