Collection HMM

The GyDB collection is a non-redundant database of manually refined multiple alignments, hidden markov model profiles, and majority-rule consensus sequences based on all currently known protein domains of the distinct mobile genetic elements and related host genes classified at GyDB.Alignments are available in six formats: Fasta, Pir, Msf, Stockholm, Clustal and Phylip. Hidden markov model profiles and majority-rule consensus (MRC) sequences were constructed based on each protein domain consensus accepted per monophyletic group of LTR retroelements and protein domain.

The collection is divided in three sections as follows:
If you want to download the whole GyDB collection, click here.

Citation:
LLORENS, C., MUNOZ-POMER, A., FUTAMI, R., and MOYA, A. The GyDB Collection of Viral and Mobile Genetic Element Models In Biotechvana Bioinformatics 2008, Biotechvana, Valencia. Computational Resources: GyDB collection
HMM Profiles
 
Gag
Protease
Reverse_Transcriptase
Ribonuclease_H
Integrase
Chromodomain
Env
dUTPase
Accessory_proteins
Aphid_transmission_factor
Movement_protein
Transactivator/viroplasmin_protein
Virion_associated_protein
 


Gag

  • GAG_412_mdg1
  • GAG_alpharetroviridae
  • GAG_athila
  • GAG_betaretroviridae
  • GAG_cer2_3
  • GAG_crm
  • GAG_reina
  • GAG_del
  • GAG_galadriel
  • GAG_deltaretroviridae
  • GAG_gammaretroviridae
  • GAG_lentiviridae
  • GAG_micropia_mdg3
  • GAG_osvaldo
  • GAG_spumaretroviridae
  • GAG_tat
  • GAG_TF
  • GAG_csrn1
  • GAG_1731
  • GAG_17_6
  • GAG_a_clade
  • GAG_b_clade
  • GAG_bel
  • GAG_codi_c
  • GAG_codi_d
  • GAG_codi_I
  • GAG_codi_II
  • GAG_copia
  • GAG_epsilonretroviridae
  • GAG_galea
  • GAG_gmr1
  • GAG_gypsy
  • GAG_hydra
  • GAG_maggy
  • GAG_oryco
  • GAG_pao
  • GAG_pCretro
  • GAG_pseudovirus
  • GAG_pyggy
  • GAG_pyret
  • GAG_retrofit
  • GAG_sinbad
  • GAG_sire
  • GAG_suzu
  • GAG_tas
  • GAG_tork
  • GAG_v_clade
  • GAGCOAT_caulimovirus
  • GAGCOAT_cavemovirus
  • GAGCOAT_soymovirus
  • GAGCOAT_badnavirus


  • Protease

  • AP_DTG_ILG_template
  • AP_micropia_mdg3
  • AP_alpharetroviridae
  • AP_athila
  • AP_betaretroviridae
  • AP_cer2_3
  • AP_bel
  • AP_crm
  • AP_reina
  • AP_del
  • AP_galadriel
  • AP_cog3577
  • AP_cog5550
  • AP_ddi
  • AP_deltaretroviridae
  • AP_gammaretroviridae
  • AP_lentiviridae
  • AP_nix1
  • AP_osvaldo
  • AP_pepsins_A1a
  • AP_pepsins_A1b
  • AP_saspase
  • AP_retropepsins
  • AP_spumaretroviridae
  • AP_tat
  • AP_ty1copia
  • AP_csrn1
  • AP_1731
  • AP_17_6
  • AP_412_mdg1
  • AP_a_clade
  • AP_b_clade
  • AP_caulimoviridae_dom2
  • AP_caulimovirus
  • AP_badnavirus
  • AP_cavemovirus
  • AP_codi_c
  • AP_codi_d
  • AP_codi_I
  • AP_codi_II
  • AP_copia
  • AP_epsilonretroviridae
  • AP_galea
  • AP_gmr1
  • AP_gypsy
  • AP_hydra
  • AP_maggy
  • AP_oryco
  • AP_pao
  • AP_pseudovirus
  • AP_pyggy
  • AP_pyret
  • AP_pCretro
  • AP_retrofit
  • AP_sinbad
  • AP_sire
  • AP_soymovirus
  • AP_suzu
  • AP_tas
  • AP_TF
  • AP_tork
  • AP_v_clade


  • Reverse_Transcriptase

  • RT_412_mdg1
  • RT_alpharetroviridae
  • RT_athila
  • RT_betaretroviridae
  • RT_cer2_3
  • RT_crm
  • RT_reina
  • RT_del
  • RT_galadriel
  • RT_TF
  • RT_deltaretroviridae
  • RT_gammaretroviridae
  • RT_lentiviridae
  • RT_micropia_mdg3
  • RT_osvaldo
  • RT_spumaretroviridae
  • RT_tat
  • RT_csrn1
  • RT_1731
  • RT_17_6
  • RT_a_clade
  • RT_b_clade
  • RT_badnavirus
  • RT_bel
  • RT_caulimovirus
  • RT_cavemovirus
  • RT_codi_c
  • RT_codi_d
  • RT_codi_I
  • RT_codi_II
  • RT_copia
  • RT_epsilonretroviridae
  • RT_galea
  • RT_gmr1
  • RT_gypsy
  • RT_hydra
  • RT_maggy
  • RT_oryco
  • RT_pao
  • RT_pCretro
  • RT_pseudovirus
  • RT_pyggy
  • RT_pyret
  • RT_retrofit
  • RT_sinbad
  • RT_sire
  • RT_soymovirus
  • RT_suzu
  • RT_tas
  • RT_tork
  • RT_v_clade


  • Ribonuclease_H

  • RNaseH_412_mdg1
  • RNaseH_alpharetroviridae
  • RNaseH_athila
  • RNaseH_betaretroviridae
  • RNaseH_cer2_3
  • RNaseH_crm
  • RNaseH_reina
  • RNaseH_del
  • RNaseH_galadriel
  • RNaseH_TF
  • RNaseH_deltaretroviridae
  • RNaseH_gammaretroviridae
  • RNaseH_lentiviridae
  • RNaseH_micropia_mdg3
  • RNaseH_osvaldo
  • RNaseH_spumaretroviridae
  • RNaseH_tat
  • RNaseH_csrn1
  • RNaseH_1731
  • RNaseH_17_6
  • RNaseH_a_clade
  • RNaseH_b_clade
  • RNaseH_badnavirus
  • RNaseH_bel
  • RNaseH_caulimovirus
  • RNaseH_cavemovirus
  • RNaseH_codi_c
  • RNaseH_codi_d
  • RNaseH_codi_I
  • RNaseH_codi_II
  • RNaseH_copia
  • RNaseH_epsilonretroviridae
  • RNaseH_galea
  • RNaseH_gmr1
  • RNaseH_gypsy
  • RNaseH_hydra
  • RNaseH_maggy
  • RNaseH_oryco
  • RNaseH_pao
  • RNaseH_pCretro
  • RNaseH_pseudovirus
  • RNaseH_pyggy
  • RNaseH_pyret
  • RNaseH_retrofit
  • RNaseH_sinbad
  • RNaseH_sire
  • RNaseH_soymovirus
  • RNaseH_suzu
  • RNaseH_tas
  • RNaseH_tork
  • RNaseH_v_clade


  • Integrase

  • INT_412_mdg1
  • INT_alpharetroviridae
  • INT_athila
  • INT_betaretroviridae
  • INT_cer2_3
  • INT_crm
  • INT_reina
  • INT_del
  • INT_galadriel
  • INT_TF
  • INT_deltaretroviridae
  • INT_gammaretroviridae
  • INT_lentiviridae
  • INT_micropia_mdg3
  • INT_osvaldo
  • INT_spumaretroviridae
  • INT_tat
  • INT_csrn1
  • GIN1
  • INT_1731
  • INT_17_6
  • INT_a_clade
  • INT_b_clade
  • INT_bel
  • INT_codi_c
  • INT_codi_d
  • INT_codi_I
  • INT_codi_II
  • INT_copia
  • INT_epsilonretroviridae
  • INT_galea
  • INT_gmr1
  • INT_gypsy
  • INT_hydra
  • INT_maggy
  • INT_oryco
  • INT_pao
  • INT_pCretro
  • INT_pseudovirus
  • INT_pyggy
  • INT_pyret
  • INT_retrofit
  • INT_sinbad
  • INT_sire
  • INT_suzu
  • INT_tas
  • INT_tork
  • INT_v_clade


  • Chromodomain

  • CHR_all
  • CHR_shadow
  • CHR_retroelement


  • Env

  • ENV_alpharetroviridae
  • ENV_athila
  • ENV_B-type_betaretroviridae
  • ENV_D-type_betaretroviridae
  • ENV_deltaretroviridae
  • ENV_gammaretroviridae
  • ENV_errantiviridae
  • ENV_lentiviridae
  • ENV_retroviridae
  • ENV_spumaretroviridae
  • ENV_epsilonretroviridae
  • ENV_sire
  • ENV_tas


  • dUTPase

  • DUT_betaretroviridae
  • DUT_lentiviridae
  • DUT_caulimoviruses


  • Accessory_proteins

  • BEL1_spumaretroviridae
  • BEL2_spumaretroviridae
  • NEF_retroviridae
  • ORFQ_retroviridae
  • VIF_retroviridae
  • VIF_Q_retroviridae
  • ORFW_retroviridae
  • ORFX_betaretroviridae
  • REV_retroviridae
  • REX_retroviridae
  • ROF_retroviridae
  • SORF_retroviridae
  • TAT_retroviridae
  • TAX_retroviridae
  • TOF_retroviridae
  • VPR_VPX_retroviridae
  • VPR_retroviridae
  • VPX_retroviridae
  • ORF2_badnavirus
  • ORF6_badnavirus
  • ORFB_soymovirus
  • ORFC_soymovirus


  • Aphid_transmission_factor

  • ATF_caulimovirus


  • Movement_protein

  • MOV_badnavirus
  • MOV_caulimovirus
  • MOV_soymovirus
  • MOV_cavemovirus


  • Transactivator/viroplasmin_protein

  • TAV_caulimovirus
  • TAV_cavemovirus
  • TAV_soymovirus


  • Virion_associated_protein

  • VAP_caulimovirus
  • VAP_badnavirus





  • 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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