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Table 6 Hits to viral proteins from structural prediction analyses

From: In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function

Gene

Hit

Function

Position

Aan-MORF

Nucleoprotein, Andes virus [Atome 2; 41.16]

Nucleoprotein

NA

Regulatory protein MNT, Enterobacteria phage P22 [Atome 2; 21.14]

Gene regulation

NA

Upe-MORF

Uncharacterized protein 56B, Sulfolobus islandicus [Atome 2; 27.96]

Transcription repressor

NA

Pgr-MORF

Matrix protein 1, Influenza A virus [Atome 2; 39.16]

Matrix protein

NA

Helix-destabilizing protein, Enterobacteria phage T7 [Atome 2; 18.55]

DNA binding protein

NA

Ija-MORF

Nonstructural protein 5A, Bovine viral diarrhea virus 1-CP7 [Atome 2; 33.37]

Membrane protein

NA

Functional anti-apoptotic factor vBCL-2 homolog, Human herpesvirus 8 [Atome 2; 27.14]

Apoptosis

NA

Sca-MORF

Nonstructural protein 5A, Bovine viral diarrhea virus 1-CP7 [Atome 2; 22.35]

Membrane protein

NA

Vel-MORF

Macrophage galactose N-acetyl-galactosamine specific lectin 2 [Hhpred; 93.40]

C-type lectin

20–171

RhUL123, Macacine herpesvirus 3 [I-TASSER; TM score 0.671]

Viral life cycle

NA

Phosphoprotein, Measels virus [Atome 2; 49.33]

Unknown function

NA

Tail needle protein gp26, Enterobacteria phage P22 [Atome 2; 48.96]

Fibrous protein

NA

Qqu-MORF

Virion RNA polymerase, Bacteriophage n4 [I-TASSER; TM score 0.542]

Transferase

NA

Cmo-MORF

No hits to viral proteins

  

Hme-MORF

Nucleoprotein, Andes virus [Atome 2; 63.91]

Nucleoprotein

NA

Aan-FORF

No hits to viral proteins

  

Upe-FORF

BM2 protein, Influenza B virus (B/Taiwan/70061/2006) [Atome 2; 42.29]

Transport protein

NA

Pgr-FORF

V-cyclin, Human herpesvirus 8 [I-TASSER; norm. TM score 0.517]

Cell cycle

NA

Lco-FORF

Herpes simplex virus protein ICP47, Herpes simplex virus (type 1/strain 17) [Atome 2; 46.61]

Membrane protein

NA

Ija-FORF

Non-structural RNA-binding protein 34, Simian rotavirus A/SA11 (2) [Atome 2; 48.04, 28.60]

Translation

NA

Sca-FORF

Major capsid protein (protein P3), Enterobacteria phage PRD1 [Atome 2; 80.01]

Capsid protein

NA

Tli-FORF

Envelope protein E, Dengue virus 2 Thailand/16681/84 [Atome 2; 46.45]

Envelope protein

NA

Vel-FORF

V1V2 region of HIV-1 on 1FD6 scaffold, Human immunodeficiency virus 1 [Atome 2; 57.65]

Immune system

NA

Qqu-FORF

HIV-1 matrix protein, Human immunodeficiency virus 1 (2) [Atome 2; 83.13, 72.79]

Matrix protein

NA

Mma-FORF

ODV-E18: Occlusion-derived virus envelope protein ODV-E18 (2) [Hhpred; 72.05, 62.79]

Envelope protein

21–62

Adenovirus fibre, Human adenovirus 2 [Atome 2; 27.29]

Fibre protein

23–55

Fibre protein 2 (receptor-binding domain), Human adenovirus 41 [I-TASSER; 18.06]

Fibre protein, receptor binding

NA

NA

Cmo-FORF

Virus attachment protein globular domain (49835) SCOP seed sequence: d1h7za [Hhpred; 21.78]

Viral attachment, entry into host cell

50–68

Adenovirus fibre protein; cell receptor recognition, receptor, Human adenovirus type 3 [Hhpred; 21.71]

Fibre protein, Cell receptor recognition

44–68

Fibre protein, Human adenovirus 37 [Atome 2; 31.21]

NA

Fibre protein, Human adenovirus 2 [Atome 2; 30.90]

NA

Type 5 fibre protein, Human adenovirus 5 [Atome 2; 30.46]

NA

Fibre protein, Human adenovirus 41 [Atome 2; 24.60]

NA

Hme-FORF

Nucleoprotein, Influenza A virus [Atome 2; 80.49]

RNA binding protein

NA

Uim-HORFs

HIV-1 capsid, Human immunodeficiency virus 1 [I-TASSER; TM score 0.513]

Capsid protein

NA

Gag Polyprotein, Human immunodeficiency virus 1 [I-TASSER; TM score 0.510]

Precursor protein

NA

Capsid protein P24, Human immunodeficiency virus type 2 [I-TASSER; TM score 0.504]

Capsid protein

NA

Nucleoprotein, Andes virus [Atome 2; 44.18]

Nucleoprotein

NA

Protein ICP47, Herpes simplex virus [Atome 2; 37.48]

Membrane protein

NA

LdOrf-129 peptide, Lymantria dispar multiple nucleopolyhedrovirus (2) [BLASTP, PSIBLAST; 2e-06, 7e-10]

Structual protein

74–144

ORF-132 protein, Lymantria dispar multiple nucleopolyhedrovirus (2) [BLASTP, PSIBLAST; 4e-06, 2e-09]

Unknown

74–131

orf-126 protein, Lymantria dispar multiple nucleopolyhedrovirus [PSIBLAST; 4e-08]

Unknown

72–140

Central variable region protein, African swine fever virus [PSIBLAST; 6e-08, 7e-07]

Unknown

60–154

Central variable region protein, African swine fever virus [PSIBLAST; 7e-08]

Unknown

60–130

pB602L, African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996 [PSIBLAST; 8e-08]

Structural capsid protein, chaperone in capsid assembly (several hits)

65–153

U1, Hyposoter didymator ichnovirus [PSIBLAST; 3e-07]

Spliceosomal RNA

65–137

gp7, Salmonella phage epsilon15 [I-TASSER; norm. Z-score 1.32]

DNA transfer protein

NA

Long tail fibre protein p37, Enterobacteria phage T4 [I-TASSER; norm. Z-score 1.30]

Fibre protein

88–166

RhUL123, Macacine herpesvirus 3 [I-TASSER; TM score 0.617]

Viral life cycle

NA

Nucleoprotein, Andes virus [Atome 2; 39.59]

Nucleoporin (several hits)

NA

LdOrf-129 peptide, Lymantria dispar multiple nucleopolyhedrovirus [PSIBLAST; 8e-10]

Structual protein

NA

ORF-132 protein, Lymantria dispar multiple nucleopolyhedrovirus [PSIBLAST; 5e-09]

Unknown

NA

DNA stabilization protein, Salmonella phage HK620 [I-TASSER; Z-score 1.09]

DNA binding & stabilization

87–188

Hexon protein, Human adenovirus 5 [I-TASSER; Z-score 1.01]

Major coat protein

139–223

Human T-cell leukemia virus type II matrix protein, Human T-lymphotropic virus 2 [I-TASSER; Z-score 1.00]

Matrix protein

NA

Herpes simplex virus protein ICP47, Herpes simplex virus (type 1/strain 17) [Atome 2; 1.72]

Blocks the major histocompatibility complex class I antigen presentation pathway

NA

Lco-HORFs

Long tail fiber protein P37, Enterobacteria phage T4 [I-TASSER; Z-score 1.01]

Receptor binding viral protein

NA

Capsid protein, Rubella virus strain M33 [Atome 2; 83.05]

Capsid component

NA

VPU protein, Human immunodeficiency virus 1 [Atome 2; 43.79]

Regulates degradation of receptor molecule CD4 (several hits)

NA

Lsu-HORFs

Major capsid protein, Synechococcus phage Syn5 [I-TASSER; Z-score 1.66]

Capsid component

NA

RhUL123, Macacine herpesvirus 3 [I-TASSER; TM score 0.547]

Viral life cycle

69–195

Herpes virus major outer envelope glycoprotein (BLLF1) [BLASTP/PSIBLAST; 2.73e-03]

Envelope protein

NA

Short tail fiber protein, Enterobacteria phage T4 [I-TASSER; Z-score 2.14]

Structural protein

NA

Major capsid protein, Synechococcus phage Syn5 [I-TASSER; Z-score 2.19]

Capsid component (several hits)

NA

Coat protein, Enterobacteria phage P22 [I-TASSER; TM score 0.520]

Coat component

NA

Herpes virus major outer envelope glycoprotein (BLLF1) [BLASTP/PSIBLAST; 4.85e-04]

Envelope protein

NA

Tpa-HORF

VPU protein (Trans-membrane domain), Human immunodeficiency virus 1 [Atome 2; 33.16]

Regulates degradation of receptor molecule CD4 (several hits)

NA

Mfa-HORFs

ODV-E18: Occlusion-derived virus envelope protein ODV-E18 [Hhpred; 74.97]

Envelope protein (several hits)

33–73

Herpes_TK_C: Thymidine kinase from Herpesvirus C-terminal, Herpesvirus (2) [Hhpred; 48.70, 48.13]

ATP binding, thymidine kinase (several hits)

33–73

Adenovirus fibre, Human adenovirus 2 [Atome 2; 34.11]

Fibre protein, receptor binding (several hits)

NA

  1. Note: I-TASSER: Norm. Z-score > 1 indicates a good alignment; TM-score > 0.5 indicates a similar fold with query [46]; position = amino acid position in the query sequence; NA not applicable