Computational protocol: Adenoviral E4 34K protein interacts with virus packaging components and may serve as the putative portal

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Protocol publication

[…] E4 34K homologous proteins in 65 different human and animal AdVs were identified using NCBI BLASTp. Sequences of these proteins were aligned with E4 34K of HAdV-C5 using COBALT (Constraint Based Multiple Alignment Tool) at the NCBI website. Protein sequences of E4 34K and other portal proteins were retrieved from the NCBI website: E4 34K (AP_000228.1), phage phi29 (P04332.1), phage portal protein, SPP1 (GAP04951.1), and bacteriophage T4 Portal Protein (3JA7_L). Sequences were submitted to PSIPRED and I-TASSER through their online websites for secondary and tertiary structure predictions, respectively, . Consensus secondary structures were extracted from both prediction results. For tertiary structure prediction, protein sequences were analyzed using RaptorX Structure Prediction and I-TASSER guiding model (Phi29 was used as a template) was employed using their online programs with default settings. The final structure images were generated with MacPyMOL (v1.8.4.0). […]

Pipeline specifications

Software tools BLASTP, PSIPRED, I-TASSER, RaptorX
Applications Protein structure analysis, Amino acid sequence alignment
Organisms unidentified adenovirus, Filamentous phage, Human poliovirus 1 Mahoney