NCBI Conserved Domain Search

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Conserved domains on [gi\|111225771\|ref\|YP_716565.1\|]
hypothetical protein FRAAL6432 [Frankia alni ACN14a]

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

133472

cd01949

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1). It is widely present in bacteria and often links to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain has been suggested to be homologous to the adenylyl cyclase catalytic domain. This prediction correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesiveness in bacteria.

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

true

false

true

157

7e-30

128.09

64.97

1,349,0,102

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 350 TDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYGGE 429
cd01949        1 TDPLTGLPNRRAFEERLERLLARARRSGRPLALLLIDLDHFKQINDTYGHAAGDEVLKEVARRLRSSLRESDLVARLGGD 80

                         90       100
                 ....*....|....*....|..
gi 111225771 430 EFALLALDVRGDALADIAERLR 451
cd01949       81 EFAILLPGTDLEEAEELAERLR 102

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

110022

pfam00990

GGDEF

GGDEF domain

false

160

7e-28

121.20

65.00

1,347,0,104

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 348 AITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYG 427
pfam00990      1 AAHDPLTGLPNRRYFEEELEQELQRAQRRQSPLALLLLDLDNFKRINDTYGHAVGDEVLQEVAQRLSSSLRRSDLVARLG 80

                         90       100
                 ....*....|....*....|....
gi 111225771 428 GEEFALLALDVRGDALADIAERLR 451
pfam00990     81 GDEFAILLPDTSLEGAQELAERIR 104

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

-1

128563

smart00267

GGDEF

diguanylate cyclase

false

163

5e-27

118.50

66.87

1,345,0,109

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 346 RVAITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVAR 425
smart00267     1 RLAFRDPLTGLPNRRYFEEELEQELQRAQRQGSPFALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSSCLRPGDLLAR 80

                         90       100
                 ....*....|....*....|....*....
gi 111225771 426 YGGEEFALLALDVRGDALADIAERLRLGV 454
smart00267    81 LGGDEFALLLPETSLEEAIALAERILQQL 109

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

-1

32381

COG2199

c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]

c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction...

false

181

2e-25

112.91

68.51

1,335,7,124

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 336 RMARLEADQRRVAITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLD 415
COG2199        8 RLRKAEERLERLALHDPLTGLPNRRAFEERLERALARARRHGEPLALLLLDLDHFKQINDTYGHAAGDEVLREVARRLRS 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 111225771 416 VTRPGDVVARYGGEEFALLALDVRGDALADIAERLRLGVGREPV 459
COG2199       88 NLREGDLVARLGGDEFAVLLPGTSLEEAARLAERIRAALEEPFF 131

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

-1

129356

TIGR00254

GGDEF

diguanylate cyclase (GGDEF) domain

false

165

6e-23

105.11

69.70

3,347,1,91,438,93,6,445,99,17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 348 AITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYG 427
TIGR00254      2 AVRDPLTGLYNRRYLEEMLDSELKRARRFQRSFSVLMIDIDNFKKINDTLGHDVGDEVLREVARILQSSVRGSDVVGRYG 81

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 111225771 428 GEEFALLALDV-RGDALAdIAERLRLGVGREPVRVA 462
TIGR00254     82 GEEFVVILPGTpLEDALS-KAERLRDAINSKPIEVA 116

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

-1

133472

cd01949

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

true

false

true

157

4e-04

42.57

21.02

1,550,124,33

                         10        20        30
                 ....*....|....*....|....*....|...
gi 111225771 551 AVLPDHAGDVYALVAVADQALYAAKEAGRDRVA 583
cd01949      125 AEYPEDGEDLEELLRRADKALYQAKRSGRNRVV 157

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

-1

128563

smart00267

GGDEF

diguanylate cyclase

false

163

0.003

39.54

20.86

1,550,128,34

                         10        20        30
                 ....*....|....*....|....*....|....
gi 111225771 551 AVLPDHAGDVYALVAVADQALYAAKEAGRDRVAI 584
smart00267   129 AAYPNPGEDAEDLLKRADTALYQAKKAGRNQVAV 162

cl00291

140583

GGDEF

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue...

-1

137400

PRK09581

pleD

response regulator PleD; Reviewed

false

true

false

457

8e-25

111.16

25.16

1,347,291,115

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 348 AITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYG 427
PRK09581     292 AVTDGLTGLHNRRYFDMHLKQLIERANERGKPLSLMMLDIDHFKQVNDTYGHDAGDEVLREFAKRLRKNIRGTDLIARYG 371

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 111225771 428 GEEFALLALDVRGDALADIAERLRLGVGREPVRVA 462
PRK09581     372 GEEFVVVMPDTDIEVAIAVAERIRRKIAEEPFAIS 406

-1

33501

COG3706

PleD

Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal...

false

true

false

435

8e-25

111.17

26.44

1,344,266,115

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 345 RRVAITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVA 424
COG3706      267 QELALVDGLTGLFNRRYFDEHLADLWKRALREGRPLSLLMLDIDDFKEINDTYGHDVGDEVLRQVARRLRQTVRGLDLVA 346

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 111225771 425 RYGGEEFALLALDVRGDALADIAERLRLGVGREPV 459
COG3706      347 RYGGEEFAVVLPDTDLEAAIAIAERIRQKINELPF 381

-1

32388

COG2206

c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]

true

false

344

1e-17

87.12

35.76

2,790,185,42,832,228,80

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 791 VGKILLPPHVLARPGPLDAEEWRLIRLHPVMGATLLAQVPDL-RVEAEIIAQQREWFGGGGYPSGIAGSRIRMESRALAV 869
COG2206      186 IGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDILKDLPEFlESVRAVALRHHERWDGTGYPRGLKGEEIPLEARIIAV 265

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 111225771 870 CTAWAAMRGGRGGRDPLSGPAAREQLRAGRATQFDPTVVDVFL 912
COG2206      266 ADVYDALTSDRPYKKAKSPEEALEELRKNSGGKFDPKVVDAFL 308

-1

137576

PRK09894

hypothetical protein; Provisional

false

true

false

293

8e-17

84.76

36.52

2,350,132,25,377,157,82

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 351 DGLTGLRTRRYLEAEMRVAARRARQigSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYGGEE 430
PRK09894     133 DVLTGLPGRRVLDESFDHQLRNREP--LNLYLALLDIDRFKLVNDTYGHLIGDVVLRTLATYLASWTRPYETVYRYGGEE 210

                         90       100
                 ....*....|....*....|....*....
gi 111225771 431 FALLALDVRGDALADIAERLRLGVGREPV 459
PRK09894     211 FIIILKAATDEEACRAGERIRQLIANQAI 239

-1

33243

COG3437

Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

Response regulator containing a CheY-like receiver domain and an HD-GYP domain [...

false

true

false

360

1e-14

77.26

35.56

2,789,221,40,829,262,87

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 790 NVGKILLPPHVLARPGPLDAEEWRLIRLHPVMGATLLAQV-PDLRVEAEIIAQQREWFGGGGYPSGIAGSRIRMESRALA 868
COG3437      222 DIGKVAIPDSILLKPGKLTSEEFEIMKGHPILGAEILKSSeRLMQVAAEIARHHHERWDGSGYPDGLKGDEIPLSARIVA 301

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 111225771 869 VCTAWAAMRGGRGGRDPLSGPAAREQLRAGRATQFDPTVVDVFLALEA 916
COG3437      302 IADVFDALVSGRPYKEAMSTEEALEIIRAQSGRLFDPKLVEAFIQVED 349

-1

34606

COG5001

Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]

Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF...

false

true

false

663

2e-14

76.99

15.84

1,338,218,105

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 339 RLEADQRRVAITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTR 418
COG5001      219 RLSDENDRLANLDSLTGLPNRRRFFAELDARLAAARQSGRRLVLGVIDLDGFKPVNDAFGHATGDRLLIEVGRRLKAFDG 298

                         90       100
                 ....*....|....*....|....*
gi 111225771 419 PGDVVARYGGEEFALLALDVRGDAL 443
COG5001      299 APILAARLGGDEFALIIPALEDDAL 323

-1

137515

PRK09776

putative sensor protein; Provisional

false

true

false

1116

1e-13

73.97

9.23

1,347,687,103

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771  348 AITDGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYG 427
PRK09776      688 ASHDALTGLANRASFEKQLREALQTVNSTHQRHALVFIDLDRFKAVNDSAGHAAGDALLRELASLMLSMLRSSDVLARLG 767

                          90       100
                  ....*....|....*....|...
gi 111225771  428 GEEFALLALDVRGDALADIAERL 450
PRK09776      768 GDEFGLLLPDCNVESARFIATRI 790

-1

137662

PRK10060

RNase II stability modulator; Provisional

false

true

false

663

5e-13

72.07

17.50

4,344,233,30,376,263,74,450,339,2,455,341,8

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 345 RRVAITDGLTGLRTRRYLEAEMRVAARRARqiGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVA 424
PRK10060     234 RILANTDSITGLPNRNAIQELIDHAIAQAD--NNQVGIVYLDLDNFKKVNDAYGHMFGDQLLQDVSLAILSCLEEDQTLA 311

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 111225771 425 RYGGEEFALLALDVRGDALADIAERL--RLgvgREPVRVAL 463
PRK10060     312 RLGGDEFLVLASHTSQAALEAMASRIltRL---RLPFRIGL 349

-1

137770

PRK10245

adrA

diguanylate cyclase AdrA; Provisional

false

true

false

371

3e-12

69.15

32.08

3,338,197,12,350,212,91,441,307,9

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 339 RLEADQRRVAIT---DGLTGLRTRRYLEAEMRVAARRARQIGSGMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLD 415
PRK10245     198 KLAEHKRRLQVMstrDGMTGVYNRRHWETMLRNEFDNCRRHNRDATLLIIDIDHFKSINDTWGHDVGDEAIVALTRQLQI 277

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 111225771 416 VTRPGDVVARYGGEEFALLALDVRGD----ALADIAERL 450
PRK10245     278 TLRGSDVIGRFGGDEFAVIMSGTPAEsaitAMLRVHEGL 316

-1

138538

PRK11359

cAMP phosphodiesterase; Provisional

false

true

false

799

8e-11

64.48

12.89

2,350,378,25,379,403,78

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 351 DGLTGLRTRRYLEAEMRVAARRARQigsgMGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLDVTRPGDVVARYGGEE 430
PRK11359     379 DPMTGLPNRNNLHNYLDDLVDKAVS----PVVYLIGVDHIQDVIDSLGYAWADQALLEVVNRFREKLKPDQYLCRIEGTQ 454

                         90       100
                 ....*....|....*....|....*..
gi 111225771 431 FALLALDVRGDALADIAERLRLGVGRE 457
PRK11359     455 FVLVSLENDVSNITQIADELRNVVSKP 481

-1

137615

PRK09966

hypothetical protein; Provisional

false

true

false

407

2e-09

60.03

25.80

2,335,235,44,380,279,61

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 111225771 336 RMARLEADQRRVAITDGLTGLRTRRYLEAEMRVAARRARQIGSGmGLLLVDVDHFKSVNDRFGHPTGDQVLAEVARRLLD 415
PRK09966     236 RLQAKNAQLLRTALHDPLTGLANRAAFRSGINTLMNNSDARKTS-ALLFLDGDNFKYINDTWGHATGDRVLIEIAKRLAE 314

                         90       100
                 ....*....|....*....|....*.
gi 111225771 416 VTRPGDVVARYGGEEFALLALDVRGD 441
PRK09966     315 FGGLRHKAYRLGGDEFAMVLYDVQSE 340

-1

active site	0	10	10	true	133472	cd01949	GGDEF
I-site	1	3	3	true	133472	cd01949	GGDEF