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Protocols

CDD specifications

Information


Unique identifier OMICS_04519
Name CDD
Alternative name Conserved Domain Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 3.16
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Conserved_Domain_Database

Maintainer


  • person_outline Aron Marchler-Bauer

Additional information


https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml

Publications for Conserved Domain Database

CDD citations

 (813)
call_split

Heterologous expression of ZjOMT from Zoysia japonica in Escherichia coli confers aluminum resistance through melatonin production

2018
PLoS One
PMCID: 5937781
PMID: 29734371
DOI: 10.1371/journal.pone.0196952
call_split See protocol

[…] CR product was cloned into the pGEM-T (Promega, USA) and subsequently sequenced.CDS was predicted by DNAMAN 7 software (Lynnon Corporation). The domain of the deduced ZjOMT protein was analyzed using Conserved Domain Database (CDD) (https://www.ncbi.nlm.nih.gov/cdd). The theoretical pI and molecular weight were predicted by the ProtParam online software (http://web.expasy.org/protparam). […]

library_books

Molecular Characterization of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) Gene Family in Betula luminifera

2018
Front Plant Sci
PMCID: 5945835
PMID: 29780401
DOI: 10.3389/fpls.2018.00608

[…] onding genomic sequences using the Gene Structure Display Sever 2 (Hu et al., ; http://gsds.cbi.pku.edu.cn/). Conserved domains of BlSPLs were identified using Pfam (http://pfam.sanger.ac.uk) and the Conserved Domain Database (CDD, http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) with the expected E-value threshold of 0.01 and the maximum hits of 500 amino acids (Zhang et al., ). Sequence logo […]

call_split

The orphan germinant receptor protein GerXAO (but not GerX3b) is essential for L alanine induced germination in Clostridium botulinum Group II

2018
Sci Rep
PMCID: 5935672
PMID: 29728678
DOI: 10.1038/s41598-018-25411-x
call_split See protocol

[…] d MEGA version 6.0 and used for generation of phylogenetic trees using the Neighbour Joining option. Figtree was used for annotation of phylogenetic trees. Conserved domains were identified using the Conserved Domain Database (NCBI). […]

library_books

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

2018
Front Microbiol
PMCID: 5943533
PMID: 29774020
DOI: 10.3389/fmicb.2018.00887

[…] construct a tree using FastTree (). Representative sequences were checked by translating into amino acid sequences with CLC Sequence Viewer 7, and further confirmed by protein annotation with NCBI’s Conserved Domain Database (). An amino acid sequence-based maximum-likelihood tree was constructed to display the phylogenetic relations between these dominant representative sequences (representing t […]

call_split

The LetA/S two component system regulates transcriptomic changes that are essential for the culturability of Legionella pneumophila in water

2018
Sci Rep
PMCID: 5928044
PMID: 29712912
DOI: 10.1038/s41598-018-24263-9
call_split See protocol

[…] NCBI Conserved Domain Database (CDD https://www.ncbi.nlm.nih.gov/cdd/) was used to search for conserved protein domains that may be implicated in signal sensing within LetS. The Accession number YP_095929. […]

library_books

Two New Lytic Bacteriophages of the Myoviridae Family Against Carbapenem Resistant Acinetobacter baumannii

2018
Front Microbiol
PMCID: 5936750
PMID: 29760690
DOI: 10.3389/fmicb.2018.00850

[…] ns/motif and additional function inference were detected using InterProScan (http://www.ebi.ac.uk/interpro/search/sequence-search) (Quevillon et al., ), HMMER (https://www.ebi.ac.uk/Tools/hmmer), and Conserved Domain Database (https://www.ncbi.nlm.nih.gov/cdd) (Marchlerbauer et al., ). The ExPASy server (http://us.expasy.org/tools/protparam.html) was used to predict molecular weight and isoelectri […]

Citations

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CDD institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rockville Pike, Bethesda, MD, USA
CDD funding source(s)
Supported by Intramural Research Program of the National Library of Medicine at National Institutes of Health/DHHS.

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