https://gydb.org/index.php?action=history&feed=atom&title=Profiles 2026-06-09T15:55:06Z Revision history for this page on the wiki MediaWiki 1.35.0 https://gydb.org/index.php?title=Profiles&diff=446&oldid=prev 2010-05-13T09:22:10Z

<p></p> <p><b>New page</b></p><div>==Gag polyprotein==<br /> <br /> ===''Retroviridae''===<br /> * GAG_alpharetroviridae.hmm<br /> * GAG_betaretroviridae.hmm<br /> * GAG_gammaretroviridae.hmm<br /> * GAG_deltaretroviridae.hmm<br /> * GAG_lentiviridae.hmm<br /> * GAG_spumaretroviridae.hmm<br /> * GAG_epsilonretroviridae.hmm<br /> <br /> ===''Ty3/Gypsy''===<br /> * GAG_412/mdg1.hmm<br /> * GAG_athila.hmm<br /> * GAG_cer2-3.hmm<br /> * GAG_maggy.hmm<br /> * GAG_pyggy.hmm<br /> * GAG_pyret.hmm<br /> * GAG_crm.hmm<br /> * GAG_galadriel.hmm<br /> * GAG_del.hmm<br /> * GAG_reina.hmm<br /> * GAG_TF.hmm<br /> * GAG_17.6.hmm<br /> * GAG_gypsy.hmm<br /> * GAG_micropia/mdg3.hmm<br /> * GAG_osvaldo.hmm<br /> * GAG_tat.hmm<br /> * GAG_csrn1.hmm<br /> * GAG_gmr1.hmm<br /> * GAG_v-clade.hmm<br /> * GAG_a-clade.hmm<br /> * GAG_b-clade.hmm<br /> <br /> ===''Ty1/Copia''===<br /> * GAG_1731.hmm<br /> * GAG_pCretro.hmm<br /> * GAG_hydra.hmm<br /> * GAG_copia (hemivirus).hmm<br /> * GAG_tork.hmm<br /> * GAG_retrofit.hmm<br /> * GAG_oryco.hmm<br /> * GAG_sire.hmm<br /> * GAG_pseudovirus.hmm<br /> * GAG_codi-I.hmm<br /> * GAG_codi-II.hmm<br /> * GAG_codi-c.hmm<br /> * GAG_codi-d.hmm<br /> <br /> ===''Bel/Pao''===<br /> * GAG_bel.hmm<br /> * GAG_suzu.hmm<br /> * GAG_sinbad.hmm<br /> * GAG_pao.hmm<br /> * GAG_tas.hmm<br /> <br /> ===''Caulimoviridae''===<br /> * GAGCOAT_caulimovirus.hmm<br /> * GAGCOAT_badnavirus.hmm<br /> * GAGCOAT_cavemovirus.hmm<br /> * GAGCOAT_soymovirus.hmm<br /> <br /> ==Protease (AP) domain==<br /> * AP_DTG/ILG_template.hmm (overall clan AA consensus)<br /> <br /> ===''Retroviridae''===<br /> * AP_alpharetroviridae.hmm<br /> * AP_betaretroviridae.hmm<br /> * AP_gammaretroviridae.hmm<br /> * AP_deltaretroviridae.hmm<br /> * AP_lentiviridae.hmm<br /> * AP_spumaretroviridae.hmm<br /> * AP_epsilonretrovirudae.hmm<br /> <br /> ===''Ty3/Gypsy''===<br /> * AP_412/mdg1.hmm<br /> * AP_athila.hmm<br /> * AP_cer2-3.hmm<br /> * AP_maggy.hmm<br /> * AP_pyggy.hmm<br /> * AP_pyret.hmm<br /> * AP_crm.hmm<br /> * AP_galadriel.hmm<br /> * AP_del.hmm<br /> * AP_reina.hmm<br /> * AP_TF.hmm<br /> * AP_micropia/mdg3.hmm<br /> * AP_osvaldo.hmm<br /> * AP_tat.hmm<br /> * AP_csrn1.hmm<br /> * AP_gmr1.hmm<br /> * AP_v-clade.hmm<br /> * AP_a-clade.hmm<br /> * AP_b-clade.hmm<br /> * AP_17.6.hmm<br /> * AP_gypsy.hmm<br /> <br /> ===''Ty1/Copia''===<br /> * AP_1731.hmm<br /> * AP_pCretro.hmm<br /> * AP_hydra.hmm<br /> * AP_copia (hemivirus).hmm<br /> * AP_tork.hmm<br /> * AP_retrofit.hmm<br /> * AP_oryco.hmm<br /> * AP_sire.hmm<br /> * AP_pseudovirus.hmm<br /> * AP_codi-I.hmm<br /> * AP_codi-II.hmm<br /> * AP_codi-c.hmm<br /> * AP_codi-d.hmm<br /> <br /> ===''Bel/Pao''===<br /> * AP_bel.hmm<br /> * AP_suzu.hmm<br /> * AP_sinbad.hmm<br /> * AP_pao.hmm<br /> * AP_tas.hmm<br /> <br /> ===''Caulimoviridae''===<br /> * AP_caulimovirus.hmm<br /> * AP_badnavirus.hmm<br /> * AP_cavemovirus.hmm<br /> * AP_soymovirus.hmm<br /> * AP_caulimoviridae_dom2.hmm (second nonpol-protease domain)<br /> <br /> ===Non-viral prokaryotic clan AA proteases===<br /> * AP_cog3577.hmm<br /> * AP_cog5550.hmm<br /> <br /> ===Non-viral eukaryotic clan AA proteases===<br /> * AP_ddi.hmm<br /> * AP_nix1.hmm<br /> * AP_SASPase.hmm<br /> * AP_pepsins_A1A.hmm<br /> * AP_pepsins_A1B.hmm<br /> <br /> ==Reverse transcriptase (RT) domain==<br /> ===''Retroviridae''===<br /> * RT_alpharetroviridae.hmm<br /> * RT_betaretroviridae.hmm<br /> * RT_gammaretroviridae.hmm<br /> * RT_deltaretroviridae.hmm<br /> * RT_lentiviridae.hmm<br /> * RT_spumaretroviridae.hmm<br /> * RT_epsilonretrovirudae.hmm<br /> <br /> ===''Ty3/Gypsy''===<br /> * RT_412/mdg1.hmm<br /> * RT_athila.hmm<br /> * RT_cer2-3.hmm<br /> * RT_maggy.hmm<br /> * RT_pyggy.hmm<br /> * RT_pyret.hmm<br /> * RT_crm.hmm<br /> * RT_galadriel.hmm<br /> * RT_del.hmm<br /> * RT_reina.hmm<br /> * RT_TF.hmm<br /> * RT_micropia/mdg3.hmm<br /> * RT_osvaldo.hmm<br /> * RT_tat.hmm<br /> * RT_csrn1.hmm<br /> * RT_gmr1.hmm<br /> * RT_v-clade.hmm<br /> * RT_a-clade.hmm<br /> * RT_b-clade.hmm<br /> * RT_17.6.hmm<br /> * RT_gypsy.hmm<br /> <br /> ===''Ty1/Copia''===<br /> * RT_1731.hmm<br /> * RT_pCretro.hmm<br /> * RT_hydra.hmm<br /> * RT_copia (hemivirus).hmm<br /> * RT_tork.hmm<br /> * RT_retrofit.hmm<br /> * RT_oryco.hmm<br /> * RT_sire.hmm<br /> * RT_pseudovirus.hmm<br /> * RT_codi-I.hmm<br /> * RT_codi-II.hmm<br /> * RT_codi-c.hmm<br /> * RT_codi-d.hmm<br /> <br /> ===''Bel/Pao''===<br /> * RT_bel.hmm<br /> * RT_suzu.hmm<br /> * RT_sinbad.hmm<br /> * RT_pao.hmm<br /> * RT_tas.hmm<br /> <br /> ===''Caulimoviridae''===<br /> * RT_caulimovirus.hmm<br /> * RT_badnavirus.hmm<br /> * RT_cavemovirus.hmm<br /> * RT_soymovirus.hmm<br /> <br /> ==Ribonuclease H (RNase) domain==<br /> ===''Retroviridae''===<br /> * RNase_alpharetroviridae.hmm<br /> * RNase_betaretroviridae.hmm<br /> * RNase_gammaretroviridae.hmm<br /> * RNase_deltaretroviridae.hmm<br /> * RNase_lentiviridae.hmm<br /> * RNase_spumaretroviridae.hmm<br /> * RNase_epsilonretroviridae.hmm<br /> <br /> ===''Ty3/Gypsy''===<br /> * RNase_412/mdg1.hmm<br /> * RNase_athila.hmm<br /> * RNase_cer2-3.hmm<br /> * RNase_maggy.hmm<br /> * RNase_pyggy.hmm<br /> * RNase_pyret.hmm<br /> * RNase_crm.hmm<br /> * RNase_galadriel.hmm<br /> * RNase_del.hmm<br /> * RNase_reina.hmm<br /> * RNase_TF.hmm<br /> * RNase_micropia/mdg3.hmm<br /> * RNase_osvaldo.hmm<br /> * RNase_tat.hmm<br /> * RNase_csrn1.hmm<br /> * RNase_gmr1.hmm<br /> * RNase_v-clade.hmm<br /> * RNase_a-clade.hmm<br /> * RNase_b-clade.hmm<br /> * RNase_17.6.hmm<br /> * RNase_gypsy.hmm<br /> <br /> ===''Ty1/Copia''===<br /> * RNase_1731.hmm<br /> * RNase_pCretro.hmm<br /> * RNase_hydra.hmm<br /> * RNase_copia (hemivirus).hmm<br /> * RNase_tork.hmm<br /> * RNase_retrofit.hmm<br /> * RNase_oryco.hmm<br /> * RNase_sire.hmm<br /> * RNase_pseudovirus.hmm<br /> * RNase_codi-I.hmm<br /> * RNase_codi-II.hmm<br /> * RNase_codi-c.hmm<br /> * RNase_codi-d.hmm<br /> <br /> ===''Bel/Pao''===<br /> * RNase_bel.hmm<br /> * RNase_suzu.hmm<br /> * RNase_sinbad.hmm<br /> * RNase_pao.hmm<br /> * RNase_tas.hmm<br /> <br /> ===''Caulimoviridae''===<br /> * RNase_caulimovirus.hmm<br /> * RNase_badnavirus.hmm<br /> * RNase_cavemovirus.hmm<br /> * RNase_soymovirus.hmm<br /> <br /> ==Integrase (INT) domain==<br /> ===''Retroviridae''===<br /> * INT_alpharetroviridae.hmm<br /> * INT_betaretroviridae.hmm<br /> * INT_gammaretroviridae.hmm<br /> * INT_deltaretroviridae.hmm<br /> * INT_lentiviridae.hmm<br /> * INT_spumaretroviridae.hmm<br /> * INT_epsilonretroviridae.hmm<br /> <br /> ===''Ty3/Gypsy''===<br /> * INT_412/mdg1.hmm<br /> * INT_athila.hmm<br /> * INT_cer2-3.hmm<br /> * INT_maggy.hmm<br /> * INT_pyggy.hmm<br /> * INT_pyret.hmm<br /> * INT_crm.hmm<br /> * INT_galadriel.hmm<br /> * INT_del.hmm<br /> * INT_reina.hmm<br /> * INT_TF.hmm<br /> * INT_micropia/mdg3.hmm<br /> * INT_osvaldo.hmm<br /> * INT_tat.hmm<br /> * INT_csrn1.hmm<br /> * INT_gmr1.hmm<br /> * INT_v-clade.hmm<br /> * INT_a-clade.hmm<br /> * INT_b-clade.hmm<br /> * INT_17.6.hmm<br /> * INT_gypsy.hmm<br /> <br /> ===''Ty1/Copia''===<br /> * INT_1731.hmm<br /> * INT_pCretro.hmm<br /> * INT_hydra.hmm<br /> * INT_copia (hemivirus).hmm<br /> * INT_tork.hmm<br /> * INT_retrofit.hmm<br /> * INT_oryco.hmm<br /> * INT_sire.hmm<br /> * INT_pseudovirus.hmm<br /> * INT_codi-I.hmm<br /> * INT_codi-II.hmm<br /> * INT_codi-c.hmm<br /> * INT_codi-d.hmm<br /> <br /> ===''Bel/Pao''===<br /> * INT_bel.hmm<br /> * INT_suzu.hmm<br /> * INT_sinbad.hmm<br /> * INT_pao.hmm<br /> * INT_tas.hmm<br /> <br /> ===Non-viral integrases===<br /> * GIN1.hmm<br /> <br /> ===dUTPase domain===<br /> * DUT_betaretroviridae.hmm<br /> * DUT_caulimoviridae.hmm<br /> * DUT_lentiviridae.hmm<br /> <br /> ===Chromodomain (CHR)===<br /> * CHR_all (canonical chromodomains including chromoviral-like chromodomains)<br /> * CHR_shadow (chromoshadow domains)<br /> * CHR_retroelement(''Ty1/Copia'' and ''Ty3/Gypsy'')<br /> <br /> ==Envelope (ENV) polyprotein==<br /> ===''Retroviridae''===<br /> * ENV_retroviridae.hmm (local Retroviridae consensus)<br /> * ENV_alpharetroviridae.hmm<br /> * ENV_B-type_betaretroviridae.hmm<br /> * ENV_D-type_betaretroviridae.hmm<br /> * ENV_gammaretroviridae.hmm<br /> * ENV_deltaretroviridae.hmm<br /> * ENV_lentiviridae.hmm<br /> * ENV_spumaretroviridae.hmm<br /> <br /> ===''Ty3/Gypsy''===<br /> * ENV_athila.hmm<br /> * ENV_errantiviridae.hmm<br /> <br /> ===''Ty1/Copia''===<br /> * ENV_sire.hmm<br /> <br /> ===''Bel/Pao''===<br /> * ENV_tas.hmm<br /> <br /> == Movement (MOV) protein ==<br /> * MOV_caulimovirus.hmm<br /> * MOV_badnavirus.hmm<br /> * MOV_cavemovirus.hmm<br /> * MOV_soymovirus.hmm<br /> <br /> ==Aphid transmission factor (ATF) protein==<br /> * ATF_caulimovirus.hmm<br /> <br /> ==Virion-associated protein (VAP)==<br /> * VAP_caulimovirus.hmm<br /> * VAP_badnavirus.hmm<br /> <br /> ==Transactivator/viroplasmin (TAV) protein ==<br /> * TAV_caulimovirus.hmm<br /> * TAV_cavemovirus.hmm<br /> * TAV_soymovirus.hmm<br /> <br /> ==Accessory genes==<br /> ===''Retroviridae''===<br /> * BEL1_spumaretroviridae.hmm<br /> * BEL2_spumaretroviridae.hmm<br /> * NEF_retroviridae.hmm (characteristic of primate lentiviruses)<br /> * REV_retroviridae.hmm (characteristic of lentiviruses)<br /> * REX_retroviridae.hmm (characteristic of deltaretroviruses)<br /> * ROF_retroviridae.hmm (characteristic of deltaretroviruses)<br /> * SORF_retroviridae.hmm (only present in the betaretroviruses SRV-1 and MPMV)<br /> * TAT_retroviridae.hmm (characteristic of lentiviruses)<br /> * TAX_retroviridae.hmm (characteristic of deltaretroviruses)<br /> * TOF_retroviridae.hmm (characteristic of deltaretroviruses)<br /> * ORFQ_retroviridae.hmm (VIF-like protein characteristic Visna virus-like lentiviruses)<br /> * ORFW_retroviridae.hmm (characteristic Visna virus-like lentiviruses)<br /> * ORFX_betaretroviridae.hmm<br /> * VIF_retroviridae.hmm (VIF-like protein characteristic primate-like lentiviruses)<br /> * VIF_Q_retroviridae.hmm (both VIF and ORFQ-like proteins of lentiviruses)<br /> * VPR_retroviridae.hmm (characteristic of primate lentiviruses)<br /> * VPX_retroviridae.hmm (only present in HIV-2-like lentiviruses)<br /> * VPR_VPX_retroviridae.hmm (both VPX and VPR-like proteins of primate lentiviruses)<br /> <br /> ===''Caulimoviridae''===<br /> * ORF2_badnavirus.hmm<br /> * ORF6_badnavirus.hmm<br /> * ORFB_soymovirus.hmm<br /> * ORFC_soymovirus.hmm<br /> <br /> ==Cite the Profile DataBase:==<br /> * Llorens, C., Futami, R., Bezemer, D., and A. Moya. (2008) The Gypsy Database (GyDB) of mobile genetic elements. [http://nar.oxfordjournals.org/cgi/content/abstract/gkm697?ijkey=NMX6zQ6UsIzfEVW&amp;keytype=ref Nucleic Acids Research (NAR)36 Database-Issue:38-46]</div>

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