ProteinCenter User Manual
Table of Contents

Chapter 26. Vocabulary

The following table contains a vocabulary of som of the term used in ProteinCenter

Table 26.1. Vocabulary

Word Description
protein keys (aka keys) Protein keys is the ProteinCenter internal term for all external protein record identifiers independent of source and type. The term covers GIs, accession codes, accession numbers, IPI identifiers etc.
Basket A container that holds a set of proteins picked by the user.
Cluster A group of proteins, consisting of an anchor protein plus a number of members that are similar to the anchor according to a specified similarity threshold (calculated the same way as neighbor similarity)
Dead protein A protein that is considered outdated in all external source databases.
Imported grouping A group of proteins with an anchor plus a number of members. The group and the anchor of each group is specified in the imported data file.
Neighbor Two proteins are considered neighbors, when they have more than 60% sequence identity over the length of the shortest of the two.
Outdated A protein key is considered outdated when it no longer appears in the external data source.
Protein In ProteinCenter, we define a protein as a specific amino acid sequence in a particular species. Hence, fragments of a full length sequences exists as separate protein entries. This, for example make different proteins for two sequences that only differ by the N-terminal Methionine being present or not (which is two different ways of presenting the same protein record at NCBI and UniProt, respectively.). Also, two different sequences that only differ in a single residue where this residue is unknown (an X) in one of the sequences will be considered to be different proteins. In conclusion, different proteins in ProteinCenter do not necessarily correspond to different isoforms, but only to different protein sequence records.
Protein-centric The protein is considered the basic unit of the system. All annotation, coding sequences etc. are considered information appended to the basic protein record.
Tryptic peptide A peptide sequence originating from a theoretical cleavage of a protein sequence by trypsin. Trypsin is assumed to cleave the sequence C-terminal to any K or R, i.e. no miscleaveges are taken into consideration.
GOslim Consolidated GO information. GOslim tailored to give approximately 20 broad categories within each of the three GO types "molecular function", "cellular component" and "biological process". The categories are designed to have minimal overlap to each other. Details of the categories are described in Appendix D, GOslim Categories.