GyDB org

Profiles

Gag polyprotein

Retroviridae

  • GAG_alpharetroviridae.hmm
  • GAG_betaretroviridae.hmm
  • GAG_gammaretroviridae.hmm
  • GAG_deltaretroviridae.hmm
  • GAG_lentiviridae.hmm
  • GAG_spumaretroviridae.hmm
  • GAG_epsilonretroviridae.hmm

Ty3/Gypsy

  • GAG_412/mdg1.hmm
  • GAG_athila.hmm
  • GAG_cer2-3.hmm
  • GAG_maggy.hmm
  • GAG_pyggy.hmm
  • GAG_pyret.hmm
  • GAG_crm.hmm
  • GAG_galadriel.hmm
  • GAG_del.hmm
  • GAG_reina.hmm
  • GAG_TF.hmm
  • GAG_17.6.hmm
  • GAG_gypsy.hmm
  • GAG_micropia/mdg3.hmm
  • GAG_osvaldo.hmm
  • GAG_tat.hmm
  • GAG_csrn1.hmm
  • GAG_gmr1.hmm
  • GAG_v-clade.hmm
  • GAG_a-clade.hmm
  • GAG_b-clade.hmm

Ty1/Copia

  • GAG_1731.hmm
  • GAG_pCretro.hmm
  • GAG_hydra.hmm
  • GAG_copia (hemivirus).hmm
  • GAG_tork.hmm
  • GAG_retrofit.hmm
  • GAG_oryco.hmm
  • GAG_sire.hmm
  • GAG_pseudovirus.hmm
  • GAG_codi-I.hmm
  • GAG_codi-II.hmm
  • GAG_codi-c.hmm
  • GAG_codi-d.hmm

Bel/Pao

  • GAG_bel.hmm
  • GAG_suzu.hmm
  • GAG_sinbad.hmm
  • GAG_pao.hmm
  • GAG_tas.hmm

Caulimoviridae

  • GAGCOAT_caulimovirus.hmm
  • GAGCOAT_badnavirus.hmm
  • GAGCOAT_cavemovirus.hmm
  • GAGCOAT_soymovirus.hmm

Protease (AP) domain

  • AP_DTG/ILG_template.hmm (overall clan AA consensus)

Retroviridae

  • AP_alpharetroviridae.hmm
  • AP_betaretroviridae.hmm
  • AP_gammaretroviridae.hmm
  • AP_deltaretroviridae.hmm
  • AP_lentiviridae.hmm
  • AP_spumaretroviridae.hmm
  • AP_epsilonretrovirudae.hmm

Ty3/Gypsy

  • AP_412/mdg1.hmm
  • AP_athila.hmm
  • AP_cer2-3.hmm
  • AP_maggy.hmm
  • AP_pyggy.hmm
  • AP_pyret.hmm
  • AP_crm.hmm
  • AP_galadriel.hmm
  • AP_del.hmm
  • AP_reina.hmm
  • AP_TF.hmm
  • AP_micropia/mdg3.hmm
  • AP_osvaldo.hmm
  • AP_tat.hmm
  • AP_csrn1.hmm
  • AP_gmr1.hmm
  • AP_v-clade.hmm
  • AP_a-clade.hmm
  • AP_b-clade.hmm
  • AP_17.6.hmm
  • AP_gypsy.hmm

Ty1/Copia

  • AP_1731.hmm
  • AP_pCretro.hmm
  • AP_hydra.hmm
  • AP_copia (hemivirus).hmm
  • AP_tork.hmm
  • AP_retrofit.hmm
  • AP_oryco.hmm
  • AP_sire.hmm
  • AP_pseudovirus.hmm
  • AP_codi-I.hmm
  • AP_codi-II.hmm
  • AP_codi-c.hmm
  • AP_codi-d.hmm

Bel/Pao

  • AP_bel.hmm
  • AP_suzu.hmm
  • AP_sinbad.hmm
  • AP_pao.hmm
  • AP_tas.hmm

Caulimoviridae

  • AP_caulimovirus.hmm
  • AP_badnavirus.hmm
  • AP_cavemovirus.hmm
  • AP_soymovirus.hmm
  • AP_caulimoviridae_dom2.hmm (second nonpol-protease domain)

Non-viral prokaryotic clan AA proteases

  • AP_cog3577.hmm
  • AP_cog5550.hmm

Non-viral eukaryotic clan AA proteases

  • AP_ddi.hmm
  • AP_nix1.hmm
  • AP_SASPase.hmm
  • AP_pepsins_A1A.hmm
  • AP_pepsins_A1B.hmm

Reverse transcriptase (RT) domain

Retroviridae

  • RT_alpharetroviridae.hmm
  • RT_betaretroviridae.hmm
  • RT_gammaretroviridae.hmm
  • RT_deltaretroviridae.hmm
  • RT_lentiviridae.hmm
  • RT_spumaretroviridae.hmm
  • RT_epsilonretrovirudae.hmm

Ty3/Gypsy

  • RT_412/mdg1.hmm
  • RT_athila.hmm
  • RT_cer2-3.hmm
  • RT_maggy.hmm
  • RT_pyggy.hmm
  • RT_pyret.hmm
  • RT_crm.hmm
  • RT_galadriel.hmm
  • RT_del.hmm
  • RT_reina.hmm
  • RT_TF.hmm
  • RT_micropia/mdg3.hmm
  • RT_osvaldo.hmm
  • RT_tat.hmm
  • RT_csrn1.hmm
  • RT_gmr1.hmm
  • RT_v-clade.hmm
  • RT_a-clade.hmm
  • RT_b-clade.hmm
  • RT_17.6.hmm
  • RT_gypsy.hmm

Ty1/Copia

  • RT_1731.hmm
  • RT_pCretro.hmm
  • RT_hydra.hmm
  • RT_copia (hemivirus).hmm
  • RT_tork.hmm
  • RT_retrofit.hmm
  • RT_oryco.hmm
  • RT_sire.hmm
  • RT_pseudovirus.hmm
  • RT_codi-I.hmm
  • RT_codi-II.hmm
  • RT_codi-c.hmm
  • RT_codi-d.hmm

Bel/Pao

  • RT_bel.hmm
  • RT_suzu.hmm
  • RT_sinbad.hmm
  • RT_pao.hmm
  • RT_tas.hmm

Caulimoviridae

  • RT_caulimovirus.hmm
  • RT_badnavirus.hmm
  • RT_cavemovirus.hmm
  • RT_soymovirus.hmm

Ribonuclease H (RNase) domain

Retroviridae

  • RNase_alpharetroviridae.hmm
  • RNase_betaretroviridae.hmm
  • RNase_gammaretroviridae.hmm
  • RNase_deltaretroviridae.hmm
  • RNase_lentiviridae.hmm
  • RNase_spumaretroviridae.hmm
  • RNase_epsilonretroviridae.hmm

Ty3/Gypsy

  • RNase_412/mdg1.hmm
  • RNase_athila.hmm
  • RNase_cer2-3.hmm
  • RNase_maggy.hmm
  • RNase_pyggy.hmm
  • RNase_pyret.hmm
  • RNase_crm.hmm
  • RNase_galadriel.hmm
  • RNase_del.hmm
  • RNase_reina.hmm
  • RNase_TF.hmm
  • RNase_micropia/mdg3.hmm
  • RNase_osvaldo.hmm
  • RNase_tat.hmm
  • RNase_csrn1.hmm
  • RNase_gmr1.hmm
  • RNase_v-clade.hmm
  • RNase_a-clade.hmm
  • RNase_b-clade.hmm
  • RNase_17.6.hmm
  • RNase_gypsy.hmm

Ty1/Copia

  • RNase_1731.hmm
  • RNase_pCretro.hmm
  • RNase_hydra.hmm
  • RNase_copia (hemivirus).hmm
  • RNase_tork.hmm
  • RNase_retrofit.hmm
  • RNase_oryco.hmm
  • RNase_sire.hmm
  • RNase_pseudovirus.hmm
  • RNase_codi-I.hmm
  • RNase_codi-II.hmm
  • RNase_codi-c.hmm
  • RNase_codi-d.hmm

Bel/Pao

  • RNase_bel.hmm
  • RNase_suzu.hmm
  • RNase_sinbad.hmm
  • RNase_pao.hmm
  • RNase_tas.hmm

Caulimoviridae

  • RNase_caulimovirus.hmm
  • RNase_badnavirus.hmm
  • RNase_cavemovirus.hmm
  • RNase_soymovirus.hmm

Integrase (INT) domain

Retroviridae

  • INT_alpharetroviridae.hmm
  • INT_betaretroviridae.hmm
  • INT_gammaretroviridae.hmm
  • INT_deltaretroviridae.hmm
  • INT_lentiviridae.hmm
  • INT_spumaretroviridae.hmm
  • INT_epsilonretroviridae.hmm

Ty3/Gypsy

  • INT_412/mdg1.hmm
  • INT_athila.hmm
  • INT_cer2-3.hmm
  • INT_maggy.hmm
  • INT_pyggy.hmm
  • INT_pyret.hmm
  • INT_crm.hmm
  • INT_galadriel.hmm
  • INT_del.hmm
  • INT_reina.hmm
  • INT_TF.hmm
  • INT_micropia/mdg3.hmm
  • INT_osvaldo.hmm
  • INT_tat.hmm
  • INT_csrn1.hmm
  • INT_gmr1.hmm
  • INT_v-clade.hmm
  • INT_a-clade.hmm
  • INT_b-clade.hmm
  • INT_17.6.hmm
  • INT_gypsy.hmm

Ty1/Copia

  • INT_1731.hmm
  • INT_pCretro.hmm
  • INT_hydra.hmm
  • INT_copia (hemivirus).hmm
  • INT_tork.hmm
  • INT_retrofit.hmm
  • INT_oryco.hmm
  • INT_sire.hmm
  • INT_pseudovirus.hmm
  • INT_codi-I.hmm
  • INT_codi-II.hmm
  • INT_codi-c.hmm
  • INT_codi-d.hmm

Bel/Pao

  • INT_bel.hmm
  • INT_suzu.hmm
  • INT_sinbad.hmm
  • INT_pao.hmm
  • INT_tas.hmm

Non-viral integrases

  • GIN1.hmm

dUTPase domain

  • DUT_betaretroviridae.hmm
  • DUT_caulimoviridae.hmm
  • DUT_lentiviridae.hmm

Chromodomain (CHR)

  • CHR_all (canonical chromodomains including chromoviral-like chromodomains)
  • CHR_shadow (chromoshadow domains)
  • CHR_retroelement(Ty1/Copia and Ty3/Gypsy)

Envelope (ENV) polyprotein

Retroviridae

  • ENV_retroviridae.hmm (local Retroviridae consensus)
  • ENV_alpharetroviridae.hmm
  • ENV_B-type_betaretroviridae.hmm
  • ENV_D-type_betaretroviridae.hmm
  • ENV_gammaretroviridae.hmm
  • ENV_deltaretroviridae.hmm
  • ENV_lentiviridae.hmm
  • ENV_spumaretroviridae.hmm

Ty3/Gypsy

  • ENV_athila.hmm
  • ENV_errantiviridae.hmm

Ty1/Copia

  • ENV_sire.hmm

Bel/Pao

  • ENV_tas.hmm

Movement (MOV) protein

  • MOV_caulimovirus.hmm
  • MOV_badnavirus.hmm
  • MOV_cavemovirus.hmm
  • MOV_soymovirus.hmm

Aphid transmission factor (ATF) protein

  • ATF_caulimovirus.hmm

Virion-associated protein (VAP)

  • VAP_caulimovirus.hmm
  • VAP_badnavirus.hmm

Transactivator/viroplasmin (TAV) protein

  • TAV_caulimovirus.hmm
  • TAV_cavemovirus.hmm
  • TAV_soymovirus.hmm

Accessory genes

Retroviridae

  • BEL1_spumaretroviridae.hmm
  • BEL2_spumaretroviridae.hmm
  • NEF_retroviridae.hmm (characteristic of primate lentiviruses)
  • REV_retroviridae.hmm (characteristic of lentiviruses)
  • REX_retroviridae.hmm (characteristic of deltaretroviruses)
  • ROF_retroviridae.hmm (characteristic of deltaretroviruses)
  • SORF_retroviridae.hmm (only present in the betaretroviruses SRV-1 and MPMV)
  • TAT_retroviridae.hmm (characteristic of lentiviruses)
  • TAX_retroviridae.hmm (characteristic of deltaretroviruses)
  • TOF_retroviridae.hmm (characteristic of deltaretroviruses)
  • ORFQ_retroviridae.hmm (VIF-like protein characteristic Visna virus-like lentiviruses)
  • ORFW_retroviridae.hmm (characteristic Visna virus-like lentiviruses)
  • ORFX_betaretroviridae.hmm
  • VIF_retroviridae.hmm (VIF-like protein characteristic primate-like lentiviruses)
  • VIF_Q_retroviridae.hmm (both VIF and ORFQ-like proteins of lentiviruses)
  • VPR_retroviridae.hmm (characteristic of primate lentiviruses)
  • VPX_retroviridae.hmm (only present in HIV-2-like lentiviruses)
  • VPR_VPX_retroviridae.hmm (both VPX and VPR-like proteins of primate lentiviruses)

Caulimoviridae

  • ORF2_badnavirus.hmm
  • ORF6_badnavirus.hmm
  • ORFB_soymovirus.hmm
  • ORFC_soymovirus.hmm

Cite the Profile DataBase:

Retrieved from "https://gydb.org/index.php?title=Profiles&oldid=446"


Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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