Computational protocol: The Core Components of Organelle Biogenesis and Membrane Transport in the Hydrogenosomes of Trichomonas vaginalis

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Protocol publication

[…] All of the identified protein sequences were manually annotated based on searches in the TrichDB (, Uniprot Protein knowledgebase (, NCBI ( and Pfam ( databases. The protein sequences (<1000 residues) were submitted (i) against a 90% redundancy-reduced NCBI nr database by means of simple pair-wise alignment Psi-BLAST for 8 iterations at an e-value cutoff of 10−3 and (ii) against the Pfam 23.0 A+B database of families represented by multiple sequence alignments and hidden Markov models (HMMs) at an e-value of 0.044.TargetP and SignalP, based on the combination of artificial neural networks and hidden Markov models, respectively (, together with PsortII (, were used to predict the subcellular location.An application based on the NetBeans Platform (Hunter) was used to predict the subcellular localization of proteins according to their N-terminal amino acid sequence, as previously described . The following parameters were used: (i) the presequence start motif - ML[ACGQRSTV] or MS[ILV] or MIS or MTL; (ii) a cleavage site motif - R.F[TKILFSAGQ] or R[AFNESG][TYILFSAGQ] or K[AFNESG][TYILFSAGQ] or K.F[TKILFSAGQ]. The secondary structure and topology of alpha-helix integral membrane proteins was predicted using two bioinformatic tools: TMHMM ( and Memsat3 ( determine members of protein families, a hidden Markov model analysis was performed according to the method of Likic et al. . [...] The model of TvTim44 (residues 144–326) was built using the human Tim44 structure (PDB ID: 2cw9) as a template. The alignment was constructed by MUSCLE and manually edited. The 3D structure model of TvTim 44 was built using Modeller 9v7 . The quality of the final model was checked using What Check and ProSA-web services . The electrostatic potential on the solvent-accessible surface of TvTim44 was calculated using APBS 1.3 . […]

Pipeline specifications

Software tools MUSCLE, MODELLER, WHAT_CHECK, ProSA-web
Applications Protein structure analysis, Nucleotide sequence alignment
Organisms Trichomonas vaginalis, Saccharomyces cerevisiae
Diseases Trichomonas Infections
Chemicals Adenosine Diphosphate, Adenosine Triphosphate, Hydrogen