NCBI Conserved Domain Search

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Conserved domains on [gi\|117928036\|ref\|YP_872587.1\|]
diguanylate phosphodiesterase [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

117241

pfam08668

HDOD

HDOD domain

true

false

196

5e-12

67.26

40.82

3,207,1,3,211,4,4,217,8,73

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036 208 PTLsPATVtcMELLNRLAKPDITYDELEEIVRMDVGLSYRVLRAVNSAAAGLVRPISSVREALVLLGHRQLRAWVLLMVL 287
pfam08668      2 PTL-PDVV--LRILALLEDPDVSISDIAELISRDPALTARLLRLANSAYYGFRRKISSIEQAVARLGLRTVRNLVLSLSV 78


                 ...
gi 117928036 288 ADA 290
pfam08668     79 KRI 81

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

31826

COG1639

Predicted signal transduction protein [Signal transduction mechanisms]

false

289

4e-06

47.65

25.61

1,209,22,74

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117928036 210 LSPATVTCMELLNRLAKPDITYDELEEIVRMDVGLSYRVLRAVNSAAAGLVRPISSVREALVLLGHRQLRAWVL 283
COG1639       23 LPPLPDVVLKLQKACSDPNVSLSDIAELISQDPALTARLLRLANSPYFGFPREITTLNEAIVRLGIGLVINLVL 96

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

109613

pfam00563

EAL

EAL domain

true

false

236

2e-05

45.10

97.88

11,1,5,17,18,23,13,31,37,3,34,51,24,58,79,17,75,105,63,138,169,7,145,182,12,157,195,6,164,201,4,171,205,31

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036   2 RKIAVREVYVGRQPIVD-RELTVLGYELLFR-HGP-----------HALRAAADDDRATGRIIVNTFAEL----GLQRLV 64
pfam00563      6 EALENGEFSLYFQPIVDlRTGKVLGYEALLRwQHPdgglippdeflPLAERLGLIAELDRWVLEKALAQLaewrGNALLP 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036  65 GSRLGFINVTR---------PFLVGTLPLPFAPADVVLEILETVVIDDDLLDGVRRLRAGGYRLALDDFRADDAERVRRL 135
pfam00563     86 PDLPLSVNLSPaslldpsflEALLALKQGGLPPSRLVLEITESDLDEDLRLLEALARLRSLGFRLALDDFGTGYSSLSYL 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 117928036 136 LPL-VDYVKVD------VLDQSPSAIARS-VEYCRKcSGARppaLIAERVESLPVMRDCVNLGFSYFQGYLLGRP 202
pfam00563    166 SRLpPDYIKIDrsfikdLSDPESRALLRAlIALARE-LGIK---VVAEGVETEEQLELLKELGIDYVQGYLFSKP 236

cl00290

140582

EAL

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called...

-1

32382

COG2200

Rtn

c-di-GMP phosphodiesterase class I (EAL domain) [Signal transduction mechanisms]

false

256

5e-04

40.69

91.02

11,3,11,15,18,27,13,31,45,19,50,71,24,74,104,9,83,114,46,129,164,8,139,172,6,145,185,12,157,198,8,169,206,38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036   4 IAVREVYVGRQPIVD-RELTVLGYELLFR-----HGPHALRAAADDDRATGRI-------IVNTFAELGLQRLVGSRLGF 70
COG2200       12 LENGEFSLYYQPIVDlATGRIVGYEALLRwrhpdGGLISPGEFIPLAEETGLIvelgrwvLEEACRQLRTWPRAGPLRLA 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036  71 INVT---------RPFLVGTLP-LPFAPADVVLEILETVVIDDDLLDGVRRLRAGGYRLALDDFRADDA----ERVRRLL 136
COG2200       92 VNLSpvqlrspglVDLLLRLLArLGLPPHRLVLEITESALIDDLDTALALLRQLRELGVRIALDDFGTGysslSYLKRLP 171

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 117928036 137 PlvDYVKVD-------VLDQSPSAIARS-VEYCRKCSgarpPALIAERVESLPVMRDCVNLGFSYFQGYLLGRPATVSS 207
COG2200      172 P--DILKIDrsfvrdlETDARDQAIVRAiVALAHKLG----LTVVAEGVETEEQLDLLRELGCDYLQGYLFSRPLPADA 244

cl00290

140582

EAL

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called...

-1

128367

smart00052

EAL

Putative diguanylate phosphodiesterase

false

241

0.008

36.81

28.22

6,138,168,7,145,180,7,152,189,5,157,195,6,164,201,4,171,205,31

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 117928036 139 VDYVKVD-----VLDQSPS--AIARS-VEYCRKcSGARppaLIAERVESLPVMRDCVNLGFSYFQGYLLGRP 202
smart00052   169 VDLLKIDksfvrDLQTDPEdeAIVQSiIELAQK-LGLQ---VVAEGVETPEQLDLLRSLGCDYGQGYLFSRP 236

cl00290

140582

EAL

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called...

-1

30163

cd01948

EAL

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called...

false

240

0.009

36.73

30.00

5,133,163,4,138,167,7,145,179,7,152,188,16,171,204,31

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 117928036 134 RLLPlVDYVKVD-----VLDQSPS--AIARSVEYCRKCSGARppaLIAERVESLPVMRDCVNLGFSYFQGYLLGRP 202
cd01948      164 KRLP-VDYLKIDrsfvrDIETDPEdrAIVRAIIALAHSLGLK---VVAEGVETEEQLELLRELGCDYVQGYLFSRP 235

cl00290

140582

EAL

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called...

-1

33240

COG3434

Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]

Predicted signal transduction protein containing EAL and modified HD-GYP domains [...

true

false

407

2e-59

225.16

98.28

6,6,0,28,34,29,119,154,148,14,171,162,127,298,290,84,382,379,21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036   7 REVYVGRQPIVDRELTVLGYELLFRHGP-HALRAAADDDRATGRIIVNTFAELGLQRLVGSRLGFINVTRPFLVGTLPLP 85
COG3434        1 MMSFVARQPILDRNKEVFGYELLFREGEkNKYPEDVDNSRATYRIIIEEFVIQGIDKLANGKKCFINFPEELLISDLPEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036  86 FAPADVVLEILETVVIDDDLLDGVRRLRAGGYRLALDDFRADDAERVRRLLPLVDYVKVDVLDQSPSAiARSVEYCRKCS 165
COG3434       81 LPPDKVVIEILEDCPPTEKLLSAIKELKQKGYLLALDDFIFSNVSEWKPLLPLSDIVKIDFKRVTFDK-ARLFDRDLGYI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036 166 GARppaLIAERVESLPVMRDCVNLGFSYFQGYLLGRPATVSSPTLSPATVTCMELLNRLAKPDITYDELEEIVRMDVGLS 245
COG3434      160 NKK---FLAEKVETEEEFEQAKKAGFDLFQGYFFSKPEIIKRGRLSPFLKTTIELLYEVIKPEVDVKRIENIIERDVGLS 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036 246 YRVLRAVNSAAAGLVRPISSVREALVLLGHRQLRAWVLLMVLADASDIVEEQL-SVAMTRARMCELLTAYLPGANPDAAF 324
COG3434      237 YKLLKFVNSSYPRKSKKIQSIQQAVVYLGQENIRKFVSLLAMSELSDKKPEELyKLSLTRAKFCELLAKRYSPEYSEEAF 316

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928036 325 LTGLLSSLDFLLGVPMTEVVARLPLDDTIARALVDGEGPLGEIVRIAKAYEVADLETL-----ALCPVDLADLAPAYLNA 399
COG3434      317 LIGMFSLLDELLDEDIESLVRELPISEEVVQALEKRYGELGQLLSLVELLENADWEEVlrlgnKLINTDEEKMRELYIEA 396


                 ....
gi 117928036 400 LAWS 403
COG3434      397 KEWS 400

-1