<commit_before># Domain kill list
# This list consists of Pfam and Scop profiles for viral proteins
# The primary list is used to identify potential viral genes
# The secondary list is used as supporting evidence for a viral gene
# but is not considered enough on it's own

47353	Retrovirus capsid protein C-terminal domain
47836	Retroviral matrix proteins
47943	Retrovirus capsid protein, N-terminal core domain
48145	Influenza virus matrix protein M1
48345	A virus capsid protein alpha-helical domain
49830	ENV polyprotein, receptor-binding domain
56831	Reovirus inner layer core protein p3
57987	Inovirus (filamentous phage) major coat protein
75719	Virus envelope proteins
82856	L-A virus major coat protein
PF00073	picornavirus capsid protein
PF00075	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle
PF00077	Retroviral aspartyl protease
PF00078	Reverse transcriptase (RNA-dependent DNA polymerase)
PF00429	ENV polyprotein (coat polyprotein)
PF00516	Envelope glycoprotein GP120
PF00517	Envelope Polyprotein GP41
PF00540	gag gene protein p17 (matrix protein)
PF00552	Integrase DNA binding domain
PF00607	gag gene protein p24 (core nucleocapsid protein)
PF00665	Integrase core domain
PF00665	Integrase core domain Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.
PF00718	Polyomavirus coat protein
PF00761	Polyomavirus coat protein
PF00944	Alphavirus core protein
PF00951	Arterivirus GL envelope glycoprotein
PF00952	Bunyavirus nucleocapsid (N) protein
PF00979	Reovirus outer capsid protein, Sigma 3
PF01003	Flavivirus capsid protein C
PF01004	Flavivirus envelope glycoprotein M
PF01065	Hexon, adenovirus major coat protein, N-terminal domain
PF01140	The matrix protein, p15, is encoded by the gag gene.
PF01141	Gag polyprotein, inner coat protein p12
PF01309	Equine arteritis virus small envelope glycoprotein
PF01539	Hepatitis C virus envelope glycoprotein E1
PF01542	Hepatitis C virus core protein
PF01560	Hepatitis C virus non-structural protein E2/NS1
PF01570	Flavivirus polyprotein propeptide
PF01606	Arterivirus envelope protein
PF01673	Herpesvirus putative major envelope glycoprotein
PF02022	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.
PF02093	Gag P30 core shell protein
PF02228	Major core protein p19
PF02337	Retroviral GAG p10 protein
PF02340	PRRSV putative envelope protein
PF02723	Non-structural protein NS3/Small envelope protein E
PF03056	Env gp36 protein (HERV/MMTV type)
PF03276	Spumavirus gag protein
PF03391	Nepovirus coat protein, central domain
PF03408	Foamy virus envelope protein
PF03554	UL73 viral envelope glycoprotein
PF03688	Nepovirus coat protein, C-terminal domain
PF03689	Nepovirus coat protein, N-terminal domain
PF03708	Avian retrovirus envelope protein, gp85
PF03732	Retrotransposon gag protein
PF04512	Baculovirus polyhedron envelope protein, PEP, N terminus
PF04513	Baculovirus polyhedron envelope protein, PEP, C terminus
PF04639	Baculoviral E56 protein, specific to ODV envelope
PF04850	Baculovirus E66 occlusion-derived virus envelope protein
PF05109	Herpes virus major outer envelope glycoprotein (BLLF1)
PF05274	Occlusion-derived virus envelope protein E25
PF05750	Rubella capsid protein
PF05767	Poxvirus virion envelope protein A14
PF05784	Betaherpesvirus UL82/83 protein N terminus
PF05858	Bovine immunodeficiency virus surface envelope protein (ENV)
PF06817	Reverse transcriptase thumb domain
PF07727	Reverse transcriptase (RNA-dependent DNA polymerase)
PF08705	Gag protein p6
PF08723	Gag protein p15
PF08791	Viral envelope protein
PF02813	Retroviral M domain

# secondary domains that are found in viruses but are not proof on their own:
2	50122	DNA-binding domain of retroviral integrase
2	53099	Ribonuclease H-like
2	49835	Virus attachment protein globular domain
2	PF01585	G-patch domain
2	PF08371	Phospholipase D/viral envelope
2	49749	Group II dsDNA viruses VP
2	101257	Flavivirus capsid protein C
2	103068	Arterivirus nucleocapsid protein
2	103145	Tombusvirus P19 core protein, VP19
2	103383	Antivirulence factor
2	103388	Virulence-associated V antigen
2	110304	Coronavirus RNA-binding domain
2	111474	Coronavirus S2 glycoprotein
2	116854	Avirulence protein AvrPto
2	118396	Ilarvirus coat protein N-terminal fragment
2	46919	Superfamily: N-terminal Zn binding domain of HIV integrase
2	49835	Virus attachment protein globular domain
2	49894	Baculovirus p35 protein
2	50789	Herpes virus serine proteinase, assemblin
2	51225	Fibre shaft of virus attachment proteins
2	51289	Tlp20, baculovirus telokin-like protein
2	58030	Rotavirus nonstructural proteins
2	58034	Multimerization domain of the phosphoprotein from sendai virus
2	58069	Virus ectodomain
2	58163	Viruses and virus-receptor complexes
2	58176	Reovirus components
2	58668	Hepatitis C virus N-terminal capsid protein fragment 2-45
2	75347	Rotavirus NSP2 fragment, C-terminal domain
2	88648	Group I dsDNA viruses
2	88650	Satellite viruses
2	89043	Soluble domain of poliovirus core protein 3a
2	56672	DNA/RNA polymerases
2	PF00692	dUTPase
2	50630	Acid proteases
2	51283	dUTPase-like
2	PF00098	Zinc knuckle
2	57756	Retrovirus zinc finger-like domains
2	56219	DNase I-like
2	56672	DNA/RNA polymerases
2	54334	Superantigen toxins, C-terminal domain
2	53098	Ribonuclease H-like
2	54160	Chromo domain-like
2	PF00385	'chromo' (CHRromatin Organisation MOdifier) domain
2	PF08333	Protein of unknown function (DUF1725)
2	PF03372	Endonuclease/Exonuclease/phosphatase family<commit_msg>tidy up<commit_after>#####################################################################
# Domain kill list
# This list consists of Pfam and Scop profiles for viral proteins
# The primary list is used to identify potential viral genes
# The secondary list is used as supporting evidence for a viral gene
# but is not considered enough on it's own
#####################################################################

# Primary domains
47353	Retrovirus capsid protein C-terminal domain
47836	Retroviral matrix proteins
47943	Retrovirus capsid protein, N-terminal core domain
48145	Influenza virus matrix protein M1
48345	A virus capsid protein alpha-helical domain
49830	ENV polyprotein, receptor-binding domain
56831	Reovirus inner layer core protein p3
57987	Inovirus (filamentous phage) major coat protein
75719	Virus envelope proteins
82856	L-A virus major coat protein
PF00073	picornavirus capsid protein
PF00075	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle
PF00077	Retroviral aspartyl protease
PF00078	Reverse transcriptase (RNA-dependent DNA polymerase)
PF00429	ENV polyprotein (coat polyprotein)
PF00516	Envelope glycoprotein GP120
PF00517	Envelope Polyprotein GP41
PF00540	gag gene protein p17 (matrix protein)
PF00552	Integrase DNA binding domain
PF00607	gag gene protein p24 (core nucleocapsid protein)
PF00665	Integrase core domain
PF00665	Integrase core domain Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.
PF00718	Polyomavirus coat protein
PF00761	Polyomavirus coat protein
PF00944	Alphavirus core protein
PF00951	Arterivirus GL envelope glycoprotein
PF00952	Bunyavirus nucleocapsid (N) protein
PF00979	Reovirus outer capsid protein, Sigma 3
PF01003	Flavivirus capsid protein C
PF01004	Flavivirus envelope glycoprotein M
PF01065	Hexon, adenovirus major coat protein, N-terminal domain
PF01140	The matrix protein, p15, is encoded by the gag gene.
PF01141	Gag polyprotein, inner coat protein p12
PF01309	Equine arteritis virus small envelope glycoprotein
PF01539	Hepatitis C virus envelope glycoprotein E1
PF01542	Hepatitis C virus core protein
PF01560	Hepatitis C virus non-structural protein E2/NS1
PF01570	Flavivirus polyprotein propeptide
PF01606	Arterivirus envelope protein
PF01673	Herpesvirus putative major envelope glycoprotein
PF02022	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.
PF02093	Gag P30 core shell protein
PF02228	Major core protein p19
PF02337	Retroviral GAG p10 protein
PF02340	PRRSV putative envelope protein
PF02723	Non-structural protein NS3/Small envelope protein E
PF02813	Retroviral M domain
PF03056	Env gp36 protein (HERV/MMTV type)
PF03276	Spumavirus gag protein
PF03391	Nepovirus coat protein, central domain
PF03408	Foamy virus envelope protein
PF03554	UL73 viral envelope glycoprotein
PF03688	Nepovirus coat protein, C-terminal domain
PF03689	Nepovirus coat protein, N-terminal domain
PF03708	Avian retrovirus envelope protein, gp85
PF03732	Retrotransposon gag protein
PF04512	Baculovirus polyhedron envelope protein, PEP, N terminus
PF04513	Baculovirus polyhedron envelope protein, PEP, C terminus
PF04639	Baculoviral E56 protein, specific to ODV envelope
PF04850	Baculovirus E66 occlusion-derived virus envelope protein
PF05109	Herpes virus major outer envelope glycoprotein (BLLF1)
PF05274	Occlusion-derived virus envelope protein E25
PF05750	Rubella capsid protein
PF05767	Poxvirus virion envelope protein A14
PF05784	Betaherpesvirus UL82/83 protein N terminus
PF05858	Bovine immunodeficiency virus surface envelope protein (ENV)
PF06817	Reverse transcriptase thumb domain
PF07727	Reverse transcriptase (RNA-dependent DNA polymerase)
PF08705	Gag protein p6
PF08723	Gag protein p15
PF08791	Viral envelope protein

# secondary domains that are found in viruses but are not proof on their own:
2	101257	Flavivirus capsid protein C
2	103068	Arterivirus nucleocapsid protein
2	103145	Tombusvirus P19 core protein, VP19
2	103383	Antivirulence factor
2	103388	Virulence-associated V antigen
2	110304	Coronavirus RNA-binding domain
2	111474	Coronavirus S2 glycoprotein
2	116854	Avirulence protein AvrPto
2	118396	Ilarvirus coat protein N-terminal fragment
2	46919	Superfamily: N-terminal Zn binding domain of HIV integrase
2	49749	Group II dsDNA viruses VP
2	49835	Virus attachment protein globular domain
2	49894	Baculovirus p35 protein
2	50122	DNA-binding domain of retroviral integrase
2	50630	Acid proteases
2	50789	Herpes virus serine proteinase, assemblin
2	51225	Fibre shaft of virus attachment proteins
2	51283	dUTPase-like
2	51289	Tlp20, baculovirus telokin-like protein
2	53098	Ribonuclease H-like
2	53099	Ribonuclease H-like
2	54160	Chromo domain-like
2	54334	Superantigen toxins, C-terminal domain
2	56219	DNase I-like
2	56672	DNA/RNA polymerases
2	57756	Retrovirus zinc finger-like domains
2	58030	Rotavirus nonstructural proteins
2	58034	Multimerization domain of the phosphoprotein from sendai virus
2	58069	Virus ectodomain
2	58163	Viruses and virus-receptor complexes
2	58176	Reovirus components
2	58668	Hepatitis C virus N-terminal capsid protein fragment 2-45
2	75347	Rotavirus NSP2 fragment, C-terminal domain
2	88648	Group I dsDNA viruses
2	88650	Satellite viruses
2	89043	Soluble domain of poliovirus core protein 3a
2	PF00098	Zinc knuckle
2	PF00385	'chromo' (CHRromatin Organisation MOdifier) domain
2	PF00692	dUTPase
2	PF01585	G-patch domain
2	PF03372	Endonuclease/Exonuclease/phosphatase family
2	PF08333	Protein of unknown function (DUF1725)
2	PF08371	Phospholipase D/viral envelope
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