The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

Abstract

Here, we present a major update to the SUPERFAMILY database and the webserver. We describe the addition of new SUPERFAMILY 2.0 profile HMM library containing a total of 27 623 HMMs. The database now includes Superfamily domain annotations for millions of protein sequences taken from the Universal Protein Recourse Knowledgebase (UniProtKB) and the National Center for Biotechnology Information (NCBI). This addition constitutes about 51 and 45 million distinct protein sequences obtained from UniProtKB and NCBI respectively. Currently, the database contains annotations for 63 244 and 102 151 complete genomes taken from UniProtKB and NCBI respectively. The current sequence collection and genome update is the biggest so far in the history of SUPERFAMILY updates. In order to the deal with the massive wealth of information, here we introduce a new SUPERFAMILY 2.0 webserver (http://supfam.org). Currently, the webserver mainly focuses on the search, retrieval and display of Superfamily annotation for the entire sequence and genome collection in the database.

Probing lncRNA–Protein Interactions: Data Repositories, Models, and Algorithms

“…Step 1 Downloading LPIs, lncRNA sequences, and protein sequences from NPInter (Hao et al, 2016), NONCODE (Zhao et al, 2015), and SUMPERFAMILY (Pandurangan et al, 2018), respectively.…”

Structure-based identification and functional characterization of an essential lipocalin in the malaria parasitePlasmodium falciparum

“…Database analysis on PlasmoDB (Aurrecoechea et al, 2009) revealed PF3D7_0925900 as the only gene in the genome of P. falciparum 3D7 containing a calycin and lipocalin superfamily signature (Mitchell et al, 2019;Pandurangan et al, 2019). The encoded protein of 217 amino acids length, which we term P. falciparum lipocalin (PfLCN), has an unknown function.…”

“…In contrast, low pairwise identities of 23% to 27% were observed for lipocalin-like proteins in Toxoplasma gondii (GenBank CEL71535), Neospora caninum (GenBank XP_003879719) and Hammondia hammondi (GenBank KEP62611), and blastp searches did not yield any significant sequence alignments to species outside the apicomplexan lineage, where overall pairwise sequence identities to known lipocalin proteins dropped below 20%, making it difficult to detect more distant homologous proteins at the sequence level. Therefore, we relied upon annotations based on libraries of protein signatures provided by the SUPERFAMILY and other databases integrated in InterPro to identify additional putative lipocalins (Mitchell et al, 2019;Pandurangan et al, 2019). Interestingly, when we did a comparative analysis of the genomes of other apicomplexan parasites and their closest free-living non-parasitic relatives for the presence of proteins belonging to the lipocalin (SSF50814 SUPERFAMILY identifier) and calycin (IPR012674, InterPro identifier) homologous superfamily, we found that most parasitic species encode one to three putative lipocalin-like genes only, while in most of the free living relatives a substantially higher number of putative lipocalin-like genes can be found even when different genome sizes are taken into account ( Figure S2).…”

“…Searching the PlasmoDB database (https://plasmodb.org/) for genes annotated as members of the lipocalin superfamily (SSF50814; SUPERFAMILY database (Pandurangan et al, 2019)) or the calycin homologous superfamily (IPR012674; InterPro (Mitchell et al, 2019)) revealed the protein coding gene PF3D7_0925900 as putative new lipocalin. We performed batch blastp searches of PfLCN (PF3D7_0925900) against the nr and env_nr database (Agarwala et al, 2018) using Geneious 10.2.3 (https://www.geneious.com) using an E-value of 10e-0 (BLOSUM62 substitution matrix) to identify close homologs in related apicomplexan species.…”

“…We then used the InterPro (Mitchell et al, 2019) and SUPERFAMILY 2.0 database (Pandurangan et al, 2019) to identify and count the number of lipocalin superfamily members in selected alveolate and outgroup species to perform an evolutionary analysis. The R package rotl v3.0.10 (Michonneau et al, 2016) was used to extract a phylogenetic tree from the Open Tree of Life v11.4 synthetic tree (Hinchliff et al, 2015) summarizing current phylogenetic and taxonomic information.…”