NCBI Conserved Domain Search

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Conserved domains on [gi\|108803859\|ref\|YP_643796.1\|]
metal dependent phosphohydrolase [Rubrobacter xylanophilus DSM 9941]

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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

28958

cd00077

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

true

false

true

145

3e-19

92.06

96.55

3,481,4,48,536,52,27,563,86,58

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 482 EHMREVSRIARRVGERLGLSPQELEALTYGALLHDIGKLGVPDAILNKpsalsprEYEAVKRHTEHGARILRRVRALSEA 561
cd00077        5 EHSLRVAQLARRLAEELGLSEEDIELLRLAALLHDIGKPGTPDAITEE-------ESELEKDHAIVGAEILRELLLEEVI 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 108803859 562 ML-------AVRHHHERFDGAGYPDGLQGADIPLLARIVFVADAFDSMTRSRPYRGGASRREALREI 621
cd00077       78 KLidelilaVDASHHERLDGLGYPDGLKGEEITLEARIVKLADRLDALRRDSREKRRRIAEEDLEEL 144

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

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

3e-07

52.20

68.15

3,316,0,22,338,26,43,381,73,34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 317 RDAVTGLPNRASLHRVLRKELA----YGGAAGVVSLRLGGLEDYARSQGMALSEALVRRIAGRLAGRHR----AFRYGVD 388
cd01949        1 TDPLTGLPNRRAFEERLERLLArarrSGRPLALLLIDLDHFKQINDTYGHAAGDEVLKEVARRLRSSLResdlVARLGGD 80

                         90       100
                 ....*....|....*....|....*..
gi 108803859 389 EFCLLVRGADEDRARGVARWALDVVRE 415
cd01949       81 EFAILLPGTDLEEAEELAERLRKAIEE 107

cl00291

140583

GGDEF

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

128747

smart00471

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif.

false

124

4e-15

78.49

98.39

5,476,1,25,503,26,30,541,56,19,560,79,11,577,90,33

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 477 DPELGEHMREVSRIARRVGERLGLSpqELEALTYGALLHDIGKLGVPDAILNKPSALspreyeavKRHTEHGARILRRVR 556
smart00471     2 DYHVFEHSLRVAQLAAALAEELGLL--DIELLLLAALLHDIGKPGTPDSFLVKTSVL--------EDHHFIGAEILLEEE 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108803859 557 ALSE----AMLAVRHHHERfdgagyPDGLQGADIPLLARIVFVADAFDSMTRSRPYRG 610
smart00471    72 EPRIleeiLATAILSHHER------PDGLRGEPITLEARIVKVADRLDALRRDRRYRR 123

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

110919

pfam01966

HD domain

false

108

2e-13

73.04

98.15

6,481,2,26,510,28,9,521,37,9,535,46,28,563,75,14,583,89,19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 482 EHMREVSRIARRVGERLGLSPQELEAltyGALLHDIGKlgVPDAILNKPsalspREYEAVKRHTEHGARILRRVRALSEA 561
pfam01966      3 EHSLRVALLARELAEELGLDPELLLL---AALLHDIGK--DPFGFLEKL-----EDFGIFKSHSVVGAEILRELEKRLGV 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 108803859 562 ML-AVRHHHERFDGAGYpdglqgADIPLLARIVFVADAFDSM 602
pfam01966     73 DLeLILEHHESWEGAGY------EPISLEARIVKLADRLDAL 108

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-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-07

52.81

59.12

3,316,21,22,338,47,39,377,90,38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 317 RDAVTGLPNRASLHRVLRKELA----YGGAAGVVSLRLGGLEDYARSQGMALSEALVRRIAGRLA----GRHRAFRYGVD 388
COG2199       22 HDPLTGLPNRRAFEERLERALArarrHGEPLALLLLDLDHFKQINDTYGHAAGDEVLREVARRLRsnlrEGDLVARLGGD 101

                         90       100
                 ....*....|....*....|....*..
gi 108803859 389 EFCLLVRGADEDRARGVARWALDVVRE 415
COG2199      102 EFAVLLPGTSLEEAARLAERIRAALEE 128

cl00291

140583

GGDEF

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

-1

128563

smart00267

GGDEF

diguanylate cyclase

false

163

2e-07

52.63

65.64

3,316,4,22,338,30,39,377,73,38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 317 RDAVTGLPNRASLHRVLRKELA----YGGAAGVVSLRLGGLEDYARSQGMALSEALVRRIAGRLA----GRHRAFRYGVD 388
smart00267     5 RDPLTGLPNRRYFEEELEQELQraqrQGSPFALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSsclrPGDLLARLGGD 84

                         90       100
                 ....*....|....*....|....*..
gi 108803859 389 EFCLLVRGADEDRARGVARWALDVVRE 415
smart00267    85 EFALLLPETSLEEAIALAERILQQLRE 111

cl00291

140583

GGDEF

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

-1

117241

pfam08668

HDOD

HDOD domain

false

196

5e-05

44.92

50.51

8,481,96,23,505,119,4,510,123,10,520,137,4,524,144,19,543,168,13,557,181,6,563,188,7

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 482 EHMREVSRIARRVGERLGLSPQElEALTyGALLHDIGKL----GVPD---AILNKPSALSPREYEAVKR-----HTEHGA 549
pfam08668     97 RHSLACALAARLLARRLGLDDPE-EAFT-AGLLHDIGKLillsLLPDeyeEILERVAAEGISLLEAEREllgtdHAEVGA 174

                         90       100
                 ....*....|....*....|..
gi 108803859 550 RILRRVRaLSEAML-AVRHHHE 570
pfam08668    175 ALLERWN-LPEELVeAIAYHHD 195

cl00076

140417

HDc

Metal dependent phosphohydrolases with conserved 'HD' motif

-1

110022

pfam00990

GGDEF

GGDEF domain

false

160

0.002

39.92

61.25

3,316,2,22,338,28,39,377,71,29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 317 RDAVTGLPNRASLHRVLRKELA----YGGAAGVVSLRLGGLEDYARSQGMALSEALVRRIAGRLA----GRHRAFRYGVD 388
pfam00990      3 HDPLTGLPNRRYFEEELEQELQraqrRQSPLALLLLDLDNFKRINDTYGHAVGDEVLQEVAQRLSsslrRSDLVARLGGD 82

                         90
                 ....*....|....*...
gi 108803859 389 EFCLLVRGADEDRARGVA 406
pfam00990     83 EFAILLPDTSLEGAQELA 100

cl00291

140583

GGDEF

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

-1

32388

COG2206

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

false

true

false

344

1e-52

203.06

49.42

2,475,144,90,565,235,79

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 476 RDPELGEHMREVSRIARRVGERLGLSPQELEALTYGALLHDIGKLGVPDAILNKPSALSPREYEAVKRHTEHGARILRRV 555
COG2206      145 KDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGLLHDIGKIGIPDSILNKPGKLTEEEFEIIKKHPIYGYDILKDL 224

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 556 RALSEAMLAV-RHHHERFDGAGYPDGLQGADIPLLARIVFVADAFDSMTRSRPYRGGASRREALREIAHNSGSQFDPRVV 634
COG2206      225 PEFLESVRAVaLRHHERWDGTGYPRGLKGEEIPLEARIIAVADVYDALTSDRPYKKAKSPEEALEELRKNSGGKFDPKVV 304

                        170
                 ....*....|
gi 108803859 635 DALFEVMEEL 644
COG2206      305 DAFLKALSKY 314

-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

3e-48

188.20

50.00

3,474,180,81,555,262,89,644,353,7

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 475 VRDPELGEHMREVSRIARRVGERLGLSPQELEALTYGALLHDIGKLGVPDAILNKPSALSPREYEAVKRHTEHGARILRR 554
COG3437      181 VRDYETGDHLERVAQYSELLAELLGLSEEEVDLIKKAAPLHDIGKVAIPDSILLKPGKLTSEEFEIMKGHPILGAEILKS 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 555 V-RALSEAMLAVRHHHERFDGAGYPDGLQGADIPLLARIVFVADAFDSMTRSRPYRGGASRREALREIAHNSGSQFDPRV 633
COG3437      261 SeRLMQVAAEIARHHHERWDGSGYPDGLKGDEIPLSARIVAIADVFDALVSGRPYKEAMSTEEALEIIRAQSGRLFDPKL 340

                        170       180
                 ....*....|....*....|
gi 108803859 634 VDALFEVMEEL--GRRRSAS 651
COG3437      341 VEAFIQVEDEIidIARRFAD 360

-1

31608

COG1418

Predicted HD superfamily hydrolase [General function prediction only]

false

true

false

222

2e-04

43.14

47.75

5,481,38,21,505,59,14,534,73,36,584,109,23,610,132,12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 482 EHMREVSRIARRVGERLGLSPqelEALTYGALLHDIGKlgvpdailnkpsalsPREYEAVKRHTEHGARILRRVRALSEA 561
COG1418       39 EHSLRVAYLAYRIAEEEGVDP---DLALRAALLHDIGK---------------AIDHEPGGSHAEIGAEIARKFLEDPVV 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 108803859 562 MLAVRHHHErfdgagypdglqgaDIPLLARIVFVADAFDSMTRSRPyrgGASRREALREIA 622
COG1418      101 INAIEAHHG--------------VEEIISRHSFLVAAADALSAARP---GARLQDADRLDA 144

-1

139166

PRK12705

hypothetical protein; Provisional

false

true

false

485

0.002

39.32

27.42

9,482,302,20,505,322,14,524,336,2,536,338,35,584,373,3,587,378,11,601,389,6,610,395,2,612,406,29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 483 HMREVSRIARRVGERLGLSPqelEALTYGALLHDIGKlgvpdAIlnkpsalsprEYEAVKRHTEHGARILRRVRALSEAM 562
PRK12705     303 HSLEVAFLAAILAALIGLDP---ALAKKAGLLHDIGK-----SV----------DFESDGNHVEIGAELAKKFNEPDYVV 364

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859 563 LAVRHHHERfdgagypdglqgaDIP--LLARIVFVADAfdsMTRSRPyrgGA---------SRREALREIAHNSGSQFDP 631
PRK12705     365 NAIASHHNK-------------VNPttVYSVLVQIADA---LSAARP---GArressdeyvQRLEELEQIAESFPGVEKA 425

                        170
                 ....*....|
gi 108803859 632 RVVDALFEVM 641
PRK12705     426 YAIQSGRELR 435

-1

137515

PRK09776

putative sensor protein; Provisional

false

true

false

1116

0.002

39.30

9.59

3,317,690,21,338,715,44,382,763,34

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108803859  318 DAVTGLPNRASLHRVLRKELA----YGGAAGVVSLRLGGLEDYARSQGMALSEALVRRIAGRLAGRHRA----FRYGVDE 389
PRK09776      691 DALTGLANRASFEKQLREALQtvnsTHQRHALVFIDLDRFKAVNDSAGHAAGDALLRELASLMLSMLRSsdvlARLGGDE 770

                          90       100
                  ....*....|....*....|....*..
gi 108803859  390 FCLLVRGADEDRARGVARWALDVVREV 416
PRK09776      771 FGLLLPDCNVESARFIATRIISAINDY 797

-1

Zn2+ binding site	0	4	4	true	28958	cd00077	HDc
Mg2+ binding site	1	1	1	true	28958	cd00077	HDc
active site	0	10	10	true	133472	cd01949	GGDEF
I-site	1	2	3	true	133472	cd01949	GGDEF