NCBI Conserved Domain Search

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Conserved domains on [gi\|111225890\|ref\|YP_716684.1\|]
putative adenylate cyclase [Frankia alni ACN14a]

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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

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

5e-22

102.56

79.74

5,36,33,78,118,111,22,144,133,17,163,150,33,196,184,30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890   37 AEAPASEVPERRVVTVLFGDLSDFTGWADNRDPERVGEMTDRVLAALAHEIDEVGGRVDNLTGDGIMAVFGAPTAHEDdp 116
COG2114        34 GRLLARGGAGDRRVTLLFADIVGSTELSESLGDEALVELLNLYFDAVAEVVARHGGRVVKFIGDGFLAVFGRPSPLED-- 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  117 erAVRAAAAMQETVRRLVQDTAGDsaegRLGLRVGINTGEVLAGVqaAISYTVIGDTVNTAARLSAAATIGTVYAGRETV 196
COG2114       112 --AVACALDLQLALRNPLARLRRE----SLRVRIGIHTGEVVVGN--TGGYTVVGSAVNQAARLESLAKPGQVLLSEATY 183

                         170       180       190
                  ....*....|....*....|....*....|.
gi 111225890  197 -LATRSVASWRELPDLTLKGKREPVPAYELI 226
COG2114       184 dLVRDLVDLFSGLGSHRLKGLARPVRVYQLC 214

cl00925

141019

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

-1

109276

pfam00211

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

false

185

6e-17

85.38

72.43

3,42,1,98,145,99,16,161,117,18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890   43 EVPERRVVTVLFGDLSDFTGWADNRDPERVGEMTDRVLAALAHEIDEVGGRVDNLTGDGIMAVFGAPTAHEDDPERAVRA 122
pfam00211       2 YAQSYDNVTILFADIVGFTALSSRHSPEELVRLLNDLYTRFDELLDKHGVYKVKTIGDAYMAASGLPPAAAHHAALLADM 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 111225890  123 AAAMQETVRRLVQDTAGDsaegrLGLRVGINTGEVLAGV--QAAISYTVIGDTVNTAAR 179
pfam00211      82 ALDMVETIEEVNVGHANG-----LRVRIGIHTGPVVAGVigARRPRYDVWGDTVNVASR 135

cl00925

141019

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

-1

128359

smart00044

CYCc

Adenylyl- / guanylyl cyclase, catalytic domain

false

194

9e-17

85.03

80.41

5,44,31,65,111,96,19,130,119,7,142,126,19,161,147,40

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890   45 PERRVVTVLFGDLSDFTGWADNRDPERVGEMTDRVLAALAHEIDEVGGRVDNLTGDGIMAVFGAPtaHEDDPERAVRAAA 124
smart00044     32 ESYDNVTILFTDIVGFTTLSSEATPEQVVTLLNDLYSRFDRIIDRHGGYKVKTIGDAYMVVSGLP--TEALVDHAELAAD 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  125 AMQETV----RRLVQDTagdsaEGRLGLRVGINTGEVLAGV--QAAISYTVIGDTVNTAARLSAAATIGTVYAGRETVLA 198
smart00044    110 EALDMVeslkTVLSQHR-----GNGLRVRIGIHTGPVVAGVvgITMPRYCLFGDTVNLASRMESVGDPGQILVSEETYSL 184


                  ...
gi 111225890  199 TRS 201
smart00044    185 LRR 187

cl00925

141019

Guanylate_cyc

Adenylate and Guanylate cyclase catalytic domain

-1

29151

cd00189

TPR

Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here

Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[...

true

100

0.002

40.45

94.00

3,779,5,27,812,32,34,852,66,33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  780 LGELRQKQGRTEEAAQCLLTALESARRagderaTAAALRRLGMLEYNAGRIGAAEDRYLEALTIARQvddprgVGWALQH 859
cd00189         6 LGNLYYKLGDYDEALEYYEKALELDPD------NADAYYNLAAAYYKLGKYEEALEDYEKALELDPD------NAKAYYN 73

                          90       100
                  ....*....|....*....|....*.
gi 111225890  860 LAWSATTRGDYPRAERTLREASAVFE 885
cd00189        74 LGLAYYKLGKYEEALEAYEKALELDP 99

cl02429

141413

TPR

Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[...

33687

COG3899

Predicted ATPase [General function prediction only]

true

false

849

4e-13

72.73

29.45

10,415,151,32,447,189,5,452,196,46,498,243,24,527,267,15,544,282,13,557,298,37,594,336,15,609,357,10,619,368,33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  416 RSGPILVLIDDLEWATSQLSDAIGRLASRLSG------PVLLV--LLDRAGPRLATLPRIRRIDLQSLSTEASGLLLQSH 487
COG3899       152 EEHPLVIVLEDLHWADSASLKLLQLLMDRIAIgayrdnEVLLLhpLRPTLGEILKSATNITTITLAPLSRADTNQLVAAT 231

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  488 LRGKTLEPHTR-DDLLARVHGNPFFLVELLNLLIDRrllhpGDGTGDGDQAELVLDgsLAETPLPAGVQSV---LAARID 563
COG3899       232 LGCTKLLPAPLlELIFEKTKGNPFFIEEFLKALYEE-----GLLVFNFDTGAWQCS--IASLGILATTDAVvefLAARLQ 304

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  564 DLDPVAKAVLRAAAVLGRRFPAEALPMVDER-PAEEVTRALEVLTER------QLVRPPRAAE-TRWRFVHPMARDVAYA 635
COG3899       305 KLPGTTREVLKAAACIGNRFDLDTLAALAEDsPALEAAALLDALQEGlilplsETYRFGSNVDiATYKFLHDRVQQAAYN 384

                         250
                  ....*....|....*..
gi 111225890  636 GLPKVERARRHATAARW 652
COG3899       385 LIPESQRQYLHLRIGQL 401

-1

33687

COG3899

Predicted ATPase [General function prediction only]

true

false

849

6e-10

62.33

9.54

3,242,0,24,267,24,33,301,57,24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225890  243 PFLGRDAELAVLETLFAEVVTRRSpEVALIVGEAGIGKTRLASELADRAERTPGTVALwGRTVRHGDGRGLAPLVDVVRN 322
COG3899         1 PLYGRETELAQLLAAFDRVSKGRG-EVVLVAGESGIGKSALVNEVHKPITQQRGYFIK-GKFDQFERNIPLSPLVQAFRD 78


                  ...
gi 111225890  323 ACG 325
COG3899        79 LMG 81

-1

138358

PRK11034

clpA

ATP-dependent Clp protease ATP-binding subunit; Provisional

false

true

false

758

0.003

40.21

6.86

4,232,178,8,242,186,10,254,196,3,259,199,31

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 111225890  233 VARPGLADdaPFLGRDAELAvlETLfaEVVTRRSPEVALIVGEAGIGKTRLASELADR 290
PRK11034      179 LARVGGID--PLIGREKELE--RAI--QVLCRRRKNNPLLVGESGVGKTAIAEGLAWR 230

-1

30888

COG0542

clpA

ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational...

false

true

false

786

0.005

39.52

6.49

3,233,163,7,242,170,13,259,183,31

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 111225890  234 ARPGLADdaPFLGRDAELAVLEtlfaEVVTRRSPEVALIVGEAGIGKTRLASELADR 290
COG0542       164 AREGKLD--PVIGRDEEIRRTI----QILSRRTKNNPVLVGEPGVGKTAIVEGLAQR 214

-1

131687

TIGR02639

ClpA

ATP-dependent Clp protease ATP-binding subunit clpA

false

true

false

731

0.007

38.87

6.98

4,233,175,7,242,182,10,254,192,3,259,195,31

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 111225890  234 ARPGLADdaPFLGRDAELAvlETLfaEVVTRRSPEVALIVGEAGIGKTRLASELADR 290
TIGR02639     176 AKNGKID--PLIGREDELE--RTI--QVLCRRKKNNPLLVGEPGVGKTAIAEGLALR 226

-1

TPR motif	0	12	12	true	29151	cd00189	TPR
binding surface	1	14	18	true	29151	cd00189	TPR