While many effector proteins are thought to encode a secretion signal, not all secreted proteins are effectors. Plant pathogens, parasites, and symbionts secrete effectors. The DOG Box: Finding the Tools for the Job The DOG box reveals the extended repertoire of effectors that rapidly manipulate plant development and immunity, ultimately resulting in a novel syncytial organ with reduced and fragmented vacuole (V), multiple enlarged nuclei (N), and proliferated ER, Golgi, and plastids (P). SGs release effectors (filled triangles) into the lumen of the stylet, to be delivered both in the apoplasm and across the plant plasma membrane (PM). We hypothesize that an as yet unidentified dorsal gland master regulator (DOGMR), specifically expressed in the dorsal gland cell, will recognize this motif, initiating the processes of transcription, translation, and secretion through the endoplasmic reticulum (ER) Golgi complex to secretory granules (SG). Dorsal gland-expressed effectors often contain a dorsal gland box (DOG box) in their promoter regions. Parasitic cyst nematodes contain two primary classes of gland cells (dorsal and subventral ). Terms of Use.Schematic of Plant Parasitic Nematode Effector Production and Infection. However, you can also compare a protein sequence to a DNA sequence to identify weak relationships between a protein sequence and a related protein-encoding DNA sequence.Ĭopyright © 2022 MacVector, Inc. Pairs of protein sequences can be scanned for sequence similarity to each other using the Dot-Plot functionality, in a similar way to DNA sequences. In addition to creating the corresponding DNA sequence, MacVector can also scan the sequence for the least degenerate nucleotide sequences than can be used as probes or PCR primers to identify those sequences in a genomic library.
#Macvector protein toolbox code
You can reverse translate a protein into its equivalent degenerate DNA sequence using the translation code of your choosing. MacVector ships with a number of default amino acid subsequence files derived from the popular PROSITE database.
However, you can use subsequences with complex patterns for the search - each pattern can have up to three distinct segments, separated by variable inter-segment regions, and you can control the overall similarity required for a match as well as defining residues which must be 100% conserved. MacVector can search for Amino Acid subsequences using a very similar approach to the Proteolytic Enzyme searching functionality. The results can be viewed in text or graphical format, with similar filtering options to those available for restriction enzyme searches.
MacVector provides a reference file containing all of the currently known useful proteolytic enzymes and you can add your own using the built-in editor. MacVector lets you scan a protein sequence for proteolytic enzyme cleavage sites in a similar way to searching DNA sequences for restriction sites. This output is designed so that you can copy the text and paste it into Microsoft Excel so that you can perform additional statistical analysis or combine plots for graphical display. In addition to the graphical display, the results can be viewed in tab-delimited text format. As with the DNA coding preference plots, you can zoom in to the residue level to closely examine interesting regions. The results can be viewed graphically using filled plots so that you can see at a glance if a protein is above or below the average for the displayed analysis. The available algorithms in the Protein Analysis Toolbox are: All are accessed through a single Protein Profile Analysis dialog. These range from simple composition reports (counts of each amino acid, pI and molecular weight) to hydrophobicity, antigenicity and secondary structure predictions. MacVector provides a variety of algorithms that you can use to analyze the composition of protein sequences. In addition to the single sequence analyses present below, you can also align multiple proteins using ClustalW and scan databases for related proteins over the Internet or locally on your own file system. MacVector provides a wide range of tools for analyzing Protein sequences. Sequence Analysis Tools for Molecular Biologists
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