Table 1.
Retroviral HMMs from Pfam sorted according to the retroviral protein product from which they were derived.
| Protein | Pfam HMMs | ||
|---|---|---|---|
| • MA | • Gag_p10 | • Gag_p12 | • zf-CCHC_5 |
| • CA | • zf-CCHC | • Gag_p30 | • Gag_p17 |
| • NC | • Gag_p24 | • zf-H2C2 | • Gag_p19 |
| • Gag_MA | • gag_pre-integrs | • Retro_M | |
| • Retrotrans_gag | |||
| • PR | • Asp_protease_2 | • RVP | • Spuma_A9PTase |
| • gag-asp_protease | • RVP_2 | ||
| • RT | • RVT_1 | • RVT_3 | • RVT_N |
| • RVT_2 | • RVT_connect | • RVT_thumb | |
| • RH | • RNase_H | ||
| • IN | • IN_DBD_C | • Rve | • Integrase_Zn |
| • SU | • GP41 | • HERV-K_env_2 | • Env_gp36 |
| • Avian_gp85 | • MMTV_SAg | ||
| • DU | • dUTPase | ||
| • Accessory proteins | • Deltaretro_Tax | • Myc-N | • Tax |
| • F-protein | • Myc-LZ | • VPR | |
| • Other | • SPX | • Ribosomal_L22 | • UBN2_2 |
| • Borrelia_orfX | • Chromo | • UBN2_3 | |
| • Gypsy | • PHD | • Exo_endo_phos_2 | |
| • Peptidase_A17 | • PHO4 | • Ets | |
| • MRI | • G-patch | • Flu_PA | |
| • TYA | • PhoH | • RdRP_1 | |
| • Orbi_VP4 | • EXS | • Mononeg_RNA_pol | |
| • EVI2A | • Exo_endo_phos | • Flavi_NS5 | |
| • Peptidase_A2B | • Tctex-1 | • Bromo_coat | |
| • ALIX_LYPXL_bnd | • MRVI1 | • RdRP4 | |
| • Reo_sigma1 | • Pkinase_Tyr | • Peptidase_A3 | |
| • TLV_coat | • DUF1725 | • Flavi_glycop_C | |
| • DUF1011 | • DUF2155 | • BAF | |
| • HLH | • AA_permease_2 | • RNA_replicase_B | |
| • Pkinase | • Cupin_8 | • Birna_RdRp | |
| • Ras | • AA_permease_C | • Peptidase_C34 | |
| • bZIP_1 | • DUF4219 | • BLVR | |
| • UQ_con | |||
HMMs in the “other” category correspond to common functional motifs, non-retroviral proteins, or domains with unknown function.