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CD-Search specifications


Unique identifier OMICS_27642
Name CD-Search
Interface Web user interface
Restrictions to use None
Input data A protein or nucleotide query as accession, gi, or sequence.
Input format FASTA
Output data Three levels of detail in CD-Search results displays, types of RPS-BLAST hits, display elements, display controls and tabular list of domain hits.
Computer skills Basic
Stability Stable
Maintained Yes




  • person_outline Aron Marchler-Bauer

Publications for CD-Search

CD-Search citations


A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant

Sci Rep
PMCID: 5940819
PMID: 29740007
DOI: 10.1038/s41598-018-24999-4

[…] ( and phobius ( The prediction of transmembrane and conserved domain were performed using TMHMM ( and NCBI CD-Search ( A phylogenetic analysis of 29 secreted homologues was performed using the maximum likelihood method with MEGA 5 software. […]


Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice

Front Immunol
PMCID: 5936971
PMID: 29760697
DOI: 10.3389/fimmu.2018.00850
call_split See protocol

[…] unctionally classified according to Gene Ontology categories using the software Blast2GO basic version 4.0.7 (). Putative signal peptides and transmembrane domain(s) were predicted using the programs CD-Search tool () and SignalP (). Structural comparison of proteomic datasets was performed by all-vs-all blast in NCBI Blast + executables (v2.7.1). […]


Culturing of female bladder bacteria reveals an interconnected urogenital microbiota

Nat Commun
PMCID: 5908796
PMID: 29674608
DOI: 10.1038/s41467-018-03968-5

[…] To identify protein domains in a genome, we performed RPS-BLAST using CDD. All protein domains were classified in different functional categories using COG database and were used to perform DAPC implemented in the R package Adegenet v2.0.1. Domain enrich […]


Phyletic Distribution and Lineage Specific Domain Architectures of Archaeal Two Component Signal Transduction Systems

J Bacteriol
PMCID: 5847659
PMID: 29263101
DOI: 10.1128/JB.00681-17

[…] the combined HK lists were manually checked against the Conserved Domain Database (CDD) and InterPro database. The presence of PAS and/or GAF domains was additionally evaluated using PSI-BLAST () and CD Search (). Transmembrane segments were predicted using TMHMM ().The lists of REC domain-containing proteins encoded in each individual genome were obtained by PSI-BLAST searches of selected taxon e […]


PlMAPK10, a Mitogen Activated Protein Kinase (MAPK) in Peronophythora litchii, Is Required for Mycelial Growth, Sporulation, Laccase Activity, and Plant Infection

Front Microbiol
PMCID: 5852060
PMID: 29568294
DOI: 10.3389/fmicb.2018.00426

[…] encodes a protein of 1082 amino acids. We predicted a typically conservative serine/threonine protein kinase catalytic (STKc) MAPK domain (E = 8.14e-143; amino acids 748–1083) in PlMAPK10, using the CD-Search program on NCBI website. Sequence conservation between full-length PlMAPK10 protein and its orthologs in P. sojae, P. infestans, and P. parasitica is 85, 90, and 90%, respectively. We also n […]


Old Yellow Enzyme from Trypanosoma cruzi Exhibits In Vivo Prostaglandin F2α Synthase Activity and Has a Key Role in Parasite Infection and Drug Susceptibility

Front Immunol
PMCID: 5845897
PMID: 29563916
DOI: 10.3389/fimmu.2018.00456

[…] proteins annotated as Old Yellow Enzymes in the KEGG Orthology database and manually recovered from published studies (multiple sequence alignment is shown in Figure in Supplementary Material). NCBI-CD search () and Pfam () were used to confirm the presence of the characteristic protein domains (“TIM_phosphate_binding superfamily” and “Oxidored_FMN”) in the selected group of protein sequences. Th […]


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

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