| IPR007081 | RNA polymerase Rpb1, domain 5 | Domain |
| IPR045867 | DNA-directed RNA polymerase, subunit beta-prime | Family |
| IPR007075 | RNA polymerase Rpb1, domain 6 | Domain |
| IPR000684 | RNA polymerase II, heptapeptide repeat, eukaryotic | Repeat |
| IPR007083 | RNA polymerase Rpb1, domain 4 | Domain |
| IPR044893 | RNA polymerase Rpb1, clamp domain superfamily | Homologous Superfamily |
| IPR006592 | RNA polymerase, N-terminal | Domain |
| IPR007066 | RNA polymerase Rpb1, domain 3 | Domain |
| IPR007073 | RNA polymerase Rpb1, domain 7 | Domain |
| IPR042102 | RNA polymerase Rpb1, domain 3 superfamily | Homologous Superfamily |
| IPR038593 | RNA polymerase Rpb1, domain 7 superfamily | Homologous Superfamily |
| IPR000722 | RNA polymerase, alpha subunit | Domain |
| IPR038120 | RNA polymerase Rpb1, funnel domain superfamily | Homologous Superfamily |
| IPR007080 | RNA polymerase Rpb1, domain 1 | Domain |
| IPR023580 | RNA polymerase subunit RPB10 | Homologous Superfamily |
| IPR020789 | RNA polymerases, subunit N, zinc binding site | Binding Site |
| IPR000268 | DNA-directed RNA polymerase subunit RPABC5/Rpb10 | Family |
| IPR009025 | DNA-directed RNA polymerase, RBP11-like dimerisation domain | Domain |
| IPR037685 | RNA polymerase RBP11 | Family |
| IPR022905 | DNA-directed RNA polymerase subunit Rpo11-like | Family |
| IPR036603 | RNA polymerase, RBP11-like subunit | Homologous Superfamily |
| IPR008193 | DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site | Conserved Site |
| IPR006591 | RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 | Family |
| IPR029040 | RNA polymerase subunit RPABC4/transcription elongation factor Spt4 | Homologous Superfamily |
| IPR039747 | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | Family |
P [auth a], T [auth e] | IPR009072 | Histone-fold | Homologous Superfamily |
P [auth a], T [auth e] | IPR007125 | Histone H2A/H2B/H3 | Domain |
P [auth a], T [auth e] | IPR000164 | Histone H3/CENP-A | Family |
Q [auth b], U [auth f] | IPR009072 | Histone-fold | Homologous Superfamily |
Q [auth b], U [auth f] | IPR035425 | CENP-T/Histone H4, histone fold | Domain |
Q [auth b], U [auth f] | IPR001951 | Histone H4 | Family |
Q [auth b], U [auth f] | IPR019809 | Histone H4, conserved site | Conserved Site |
Q [auth b], U [auth f] | IPR004823 | TATA box binding protein associated factor (TAF), histone-like fold domain | Domain |
R [auth c], V [auth g] | IPR009072 | Histone-fold | Homologous Superfamily |
R [auth c], V [auth g] | IPR007125 | Histone H2A/H2B/H3 | Domain |
R [auth c], V [auth g] | IPR002119 | Histone H2A | Family |
R [auth c], V [auth g] | IPR032454 | Histone H2A, C-terminal domain | Domain |
R [auth c], V [auth g] | IPR032458 | Histone H2A conserved site | Conserved Site |
S [auth d], W [auth h] | IPR009072 | Histone-fold | Homologous Superfamily |
S [auth d], W [auth h] | IPR007125 | Histone H2A/H2B/H3 | Domain |
S [auth d], W [auth h] | IPR000558 | Histone H2B | Family |
S [auth d], W [auth h] | IPR055333 | Histone H2B, conserved site | Conserved Site |
| IPR007120 | DNA-directed RNA polymerase, subunit 2, hybrid-binding domain | Domain |
| IPR007121 | RNA polymerase, beta subunit, conserved site | Conserved Site |
| IPR007646 | RNA polymerase Rpb2, domain 4 | Domain |
| IPR007647 | RNA polymerase Rpb2, domain 5 | Domain |
| IPR014724 | RNA polymerase Rpb2, OB-fold | Homologous Superfamily |
| IPR007642 | RNA polymerase Rpb2, domain 2 | Domain |
| IPR015712 | DNA-directed RNA polymerase, subunit 2 | Family |
| IPR037033 | DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily | Homologous Superfamily |
| IPR037034 | RNA polymerase Rpb2, domain 2 superfamily | Homologous Superfamily |
| IPR007645 | RNA polymerase Rpb2, domain 3 | Domain |
| IPR007644 | RNA polymerase, beta subunit, protrusion | Domain |
| IPR007641 | RNA polymerase Rpb2, domain 7 | Domain |
| IPR011262 | DNA-directed RNA polymerase, insert domain | Domain |
| IPR011263 | DNA-directed RNA polymerase, RpoA/D/Rpb3-type | Domain |
| IPR050518 | Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit | Family |
| IPR022842 | DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 | Family |
| IPR036643 | DNA-directed RNA polymerase, insert domain superfamily | Homologous Superfamily |
| IPR001514 | DNA-directed RNA polymerase, 30-40kDa subunit, conserved site | Conserved Site |
| IPR036603 | RNA polymerase, RBP11-like subunit | Homologous Superfamily |
| IPR005574 | RNA polymerase subunit Rpb4/RPC9 | Family |
| IPR010997 | HRDC-like superfamily | Homologous Superfamily |
| IPR006590 | RNA polymerase Rpb4/RPC9, core | Domain |
| IPR038324 | Rpb4/RPC9 superfamily | Homologous Superfamily |
| IPR045222 | DNA-directed RNA polymerase II subunit Rpb4-like | Family |
| IPR014381 | DNA-directed RNA polymerase subunit Rpo5/Rpb5 | Family |
| IPR036710 | RNA polymerase Rpb5, N-terminal domain superfamily | Homologous Superfamily |
| IPR035913 | RPB5-like RNA polymerase subunit superfamily | Homologous Superfamily |
| IPR000783 | RNA polymerase, subunit H/Rpb5 C-terminal | Domain |
| IPR020608 | RNA polymerase, subunit H/Rpb5, conserved site | Conserved Site |
| IPR005571 | RNA polymerase, Rpb5, N-terminal | Domain |
| IPR020708 | DNA-directed RNA polymerase, 14-18kDa subunit, conserved site | Conserved Site |
| IPR028363 | DNA-directed RNA polymerase, subunit RPB6 | Family |
| IPR006110 | RNA polymerase, subunit omega/Rpo6/RPB6 | Family |
| IPR036161 | RPB6/omega subunit-like superfamily | Homologous Superfamily |
| IPR006111 | Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit | Family |
| IPR003029 | S1 domain | Domain |
| IPR045113 | RNA polymerase subunit Rpb7-like | Family |
| IPR005576 | RNA polymerase Rpb7-like , N-terminal | Domain |
| IPR036898 | RNA polymerase Rpb7-like, N-terminal domain superfamily | Homologous Superfamily |
| IPR012340 | Nucleic acid-binding, OB-fold | Homologous Superfamily |
| IPR005570 | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | Family |
| IPR012340 | Nucleic acid-binding, OB-fold | Homologous Superfamily |
| IPR001529 | DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbon | Domain |
| IPR012164 | DNA-directed RNA polymerase subunit/transcription factor S | Family |
| IPR001222 | Zinc finger, TFIIS-type | Domain |
| IPR034012 | Pol II subunit B9, C-terminal zinc ribbon | Domain |
| IPR019761 | DNA-directed RNA polymerase M, 15kDa subunit, conserved site | Conserved Site |