Functional annotation prediction for protein sequences

Association·arcadia

Association linking computational prediction of protein domains and function using Interproscan, USPNet, metapredict, UniProt, MMseqs2, and database filtering.

Confidence

70%

active

Evidence Quote

“Functional prediction and localization via Interproscan, USPNet, metapredict, UniProt, MMseqs2, PDB, and AlphaFold DB”

Relationship

functional annotation tools predicts protein function classification

Arguments

TM-score (structural similarity)subject

TM-score (structural similarity)object

Connections (6)

Reasoning chain for computational protein annotationInferenceChain

Inference chain for Asgard archaea's role in eukaryogenesisInferenceChain

Asgard archaea encode eukaryotic cytoskeleton and ESCRT systems enabling eukaryogenesisInferenceChain

Integrating structure-based and phylogenetic prediction for protein annotationInferenceChain

Rationale for multi-tool phylogenetic and protein annotation pipelineInferenceChain

Evidence

“Reference describing MMseqs2 for protein sequence search on large data sets.”

Steinegger M & Söding J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets doi:10.1038/nbt.3988 ↗

“Reference for BLAST algorithm for local sequence alignment.”

(1990). Basic local alignment search tool doi:10.1016/s0022-2836(05)80360-2 ↗

“Reference to AlphaFold Protein Structure Database publication”

Varadi M et al. (2021). AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models doi:10.1093/nar/gkab1061 ↗

“Reference to a study on Asgard archaea's contribution to eukaryogenesis”

(2024). Dominant contribution of Asgard archaea to eukaryogenesis doi:10.1101/2024.10.14.618318 ↗

“Reference to a study on the closest relatives to eukaryotes being simple syntrophic archaea”

Imachi H et al. (2025). Eukaryotes’ closest relatives are internally simple syntrophic archaea doi:10.1101/2025.02.26.640444 ↗

“Reference to a study addressing diverse ancestries and symbiotic interactions in eukaryogenesis”

Bernabeu M et al. (2024). Diverse ancestries reveal complex symbiotic interactions during eukaryogenesis doi:10.1101/2024.10.14.618062 ↗

“Reference to a study using structural analysis to infer eukaryotic complexity in Asgard archaea”

Köstlbacher S et al. (2024). Structure-based inference of eukaryotic complexity in Asgard archaea doi:10.1101/2024.07.03.601958 ↗

“Reference to a study on archaeal actins and cytoskeleton origins”

Charles-Orszag A et al. (2024). Archaeal actins and the origin of a multi-functional cytoskeleton doi:10.1128/jb.00348-23 ↗

“Evidence summarizing recent studies on the dominant role of Asgard archaea and complex ancestries in the origin of eukaryotes.”

Dominant contribution of Asgard archaea to eukaryogenesis

“Reference to study on giant virus diversity and their host interactions identified via global metagenomics.”

Schulz F et al. (2020). Giant virus diversity and host interactions through global metagenomics doi:10.1038/s41586-020-1957-x ↗

“Reference to a study on Mimivirus and Mimiviridae host range and biology.”

Claverie J-M et al. (2009). Mimivirus and Mimiviridae: Giant viruses with an increasing number of potential hosts, including corals and sponges doi:10.1016/j.jip.2009.03.011 ↗

“Reference to a study on the actin cytoskeleton in Asgard archaea.”

Rodrigues-Oliveira T et al. (2022). Actin cytoskeleton and complex cell architecture in an Asgard archaeon doi:10.1038/s41586-022-05550-y ↗

“Reference to a study on Asgard archaeal ESCRT-III system and its implication in eukaryogenesis.”

Melnikov N et al. (2022). The Asgard archaeal ESCRT-III system forms helical filaments and remodels eukaryotic membranes, shedding light on the emergence of eukaryogenesis doi:10.1101/2022.09.07.506706 ↗

“Reference to study on the presence of Arf family GTPases in Asgard archaea.”

Vargová R et al. (2024). Arf family GTPases are present in Asgard archaea doi:10.1101/2024.02.28.582541 ↗

“Reference to a study on the diversity, origin, and evolution of ESCRT systems.”

(2024). Diversity, origin, and evolution of the ESCRT systems doi:10.1128/mbio.00335-24 ↗

“Reference to InterProScan 5 for genome-scale protein function classification.”

Jones P et al. (2014). InterProScan 5: genome-scale protein function classification doi:10.1093/bioinformatics/btu031 ↗

“Reference to USPNet, a deep learning-based signal peptide prediction method.”

Shen J et al. (2023). Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model doi:10.1038/s43588-023-00576-2 ↗