NCBI Conserved Domain Search

NewSearch

CDD Home

Conserved domains on [gi\|25026866\|ref\|NP_736920.1\|]
hypothetical protein CE0310 [Corynebacterium efficiens YS-314]

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.

Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH

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

32297

COG2114

CyaA

Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]

Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction...

true

false

227

1e-24

109.88

95.15

5,308,5,38,354,43,110,466,153,19,487,172,16,504,188,33

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25026866 309 GVLQAGFNEMMRGLRERQRVRDLFGRYVGDEVARRALEerptlggeDRKVAVLFVDVIGSTTFAVNHAPEEVVEALNEFF 388
COG2114       6 NLLAKEAKVAAAGLRSDLVLRLYLARVVGRLLARGGAG--------DRRVTLLFADIVGSTELSESLGDEALVELLNLYF 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25026866 389 ERVVEVIHRNKGVINKFQGDAALAIFGAPLPLSDATGHALAAARELRIELKDLQLKAGIGVAAGHVVAGHIGGHDRfeYT 468
COG2114      78 DAVAEVVARHGGRVVKFIGDGFLAVFGRPSPLEDAVACALDLQLALRNPLARLRRESLRVRIGIHTGEVVVGNTGG--YT 155

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 25026866 469 VIGDAVNQAARLTEIAKttPGRTVTNAATLREANEaEQARWTLMKSVELRGRGEMTQLARPIRATLADR 537
COG2114     156 VVGSAVNQAARLESLAK--PGQVLLSEATYDLVRD-LVDLFSGLGSHRLKGLARPVRVYQLCHRSLRRN 221

cl00925

141019

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

-1

109276

pfam00211

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

false

185

5e-12

68.05

95.14

5,353,4,69,422,81,38,463,119,22,487,141,24,511,167,13

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25026866 354 EDRKVAVLFVDVIGSTTFAVNHAPEEVVEALNEFFERVVEVIHRNKGVINKFQGDAALAIFGAPLPLSD--------ATG 425
pfam00211     5 SYDNVTILFADIVGFTALSSRHSPEELVRLLNDLYTRFDELLDKHGVYKVKTIGDAYMAASGLPPAAAHhaalladmALD 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25026866 426 HALAAARELRIELKDLQLKAGIGVAAGHVVAGHIGghdRFEYTVIGDAVNQAARLTEIAKttPGRTVTNAATLREANEAE 505
pfam00211    85 MVETIEEVNVGHANGLRVRIGIHTGPVVAGVIGAR---RPRYDVWGDTVNVASRMESTGV--PGKIHVSEETYRLLKGEE 159

                       170       180
                ....*....|....*....|.
gi 25026866 506 QARWTL--MKSVELRGRGEMT 524
pfam00211   160 SFQFRLepRGEVPVKGKGPME 180

cl00925

141019

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

-1

128359

smart00044

CYCc

Adenylyl- / guanylyl cyclase, catalytic domain

false

194

4e-08

54.98

50.00

2,323,1,22,345,24,74

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25026866 324 ERQRVRDLFGRYVGDEVARRAL-EERPTLGGEDRKVAVLFVDVIGSTTFAVNHAPEEVVEALNEFFERVVEVIHRNKGVI 402
smart00044    2 EKRKTDRLLDQLLPASVAESLKrGGSPVPAESYDNVTILFTDIVGFTTLSSEATPEQVVTLLNDLYSRFDRIIDRHGGYK 81

                        90
                ....*....|....*..
gi 25026866 403 NKFQGDAALAIFGAPLP 419
smart00044   82 VKTIGDAYMVVSGLPTE 98

cl00925

141019

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

-1

128599

smart00304

HAMP

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

true

false

1e-06

49.56

98.11

1,275,1,52

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 25026866 276 SVVDPILELQDAIGRVRRGDNDVQVDIYDGSEIGVLQAGFNEMMRGLRERQR 327
smart00304    2 RILRPLRRLAEAAQRIADGDLTVRLPVDGRDEIGELARAFNEMADRLEETIA 53

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

2e-05

46.09

100.00

1,276,0,48

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 25026866 277 VVDPILELQDAIGRVRRGDNDVQVDIYDGSEIGVLQAGFNEMMRGLRE 324
cd06225       1 ILRPLRRLAEAAQRIAAGDLDVRLPVTGRDEIGELARAFNQMAERLRE 48

cl01054

141075

HAMP

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

-1

109717

pfam00672

HAMP

HAMP domain

false

2e-04

42.22

70.00

1,275,21,49

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 25026866 276 SVVDPILELQDAIGRVRRGDNDVQVDIYDGSEIGVLQAGFNEMMRGLRE 324
pfam00672    22 RLLRPLRRLAEAARRIASGDLDDRVPVSGPDEIGELARAFNQMADRLRE 70

cl01054

141075

HAMP

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

-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-04

41.86

9.69

3,271,299,33,304,333,23,336,356,12

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 25026866 272 LAVASVVDPILELQDAIGRVRRGDNDVQVDIYD-GSEIGVLQAGFNEMMRGLRERQRvrdlfgryvGDEVARRALEER 348
COG5000     300 AFARRIVRPIRKLIEAADEVADGDLDVQVPVRRvDEDVGRLSKAFNKMTEQLSSQQE---------ALERAKDALEQR 368

-1