| PF00193 | Xlink | Extracellular link domain | P15379 |
| PF00739 | X | Trans-activation protein X | |
| PF00752 | XPG_N | XPG N-terminal domain | P39748 |
| PF00860 | Xan_ur_permease | Permease family | Q47WB4 |
| PF00867 | XPG_I | XPG I-region | P39748 |
| PF01286 | XPA_N | XPA protein N-terminal | P23025 |
| PF01834 | XRCC1_N | XRCC1 N terminal domain | P18887 |
| PF02162 | XYPPX | XYPPX repeat (two copies) | P31356 |
| PF02625 | XdhC_CoxI | XdhC and CoxI family | Q9KBF4 |
| PF03159 | XRN_N | XRN 5'-3' exonuclease N-terminus | G0S058 |
| PF03254 | XG_FTase | Xyloglucan fucosyltransferase | Q9SWH5 |
| PF03468 | XS | XS domain | Q8VZ79 |
| PF03469 | XH | XH domain | |
| PF03894 | XFP | D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase | Q6R2Q7 |
| PF04555 | XhoI | Restriction endonuclease XhoI | |
| PF04921 | XAP5 | XAP5, circadian clock regulator C-terminal domain | |
| PF05181 | XPA_C | XPA protein C-terminus | P23025 |
| PF06505 | XylR_N | Activator of aromatic catabolism | Q43965 |
| PF06632 | XRCC4 | XRCC4 N-terminal domain | Q13426 |
| PF06955 | XET_C | Xyloglucan endo-transglycosylase (XET) C-terminus | Q07524 |
| PF07983 | X8 | X8 domain | Q06135 |
| PF08043 | Xin | Xin repeat | |
| PF08389 | Xpo1 | Exportin 1-like protein | P30822 |
| PF08814 | XisH | XisH protein | Q3M7W6 |
| PF08869 | XisI | XisI protein | B2JAN5 |
| PF09108 | Xol-1_N | Switch protein XOL-1, N-terminal | Q23229 |
| PF09109 | Xol-1_GHMP-like | Switch protein XOL-1, GHMP-like | Q23229 |
| PF09280 | XPC-binding | XPC-binding domain | P54725 |
| PF09302 | XLF | XLF N-terminal domain | Q9H9Q4 |
| PF09363 | XFP_C | XFP C-terminal domain | Q6R2Q7 |
| PF09364 | XFP_N | XFP N-terminal domain | Q6R2Q7 |
| PF09412 | XendoU | Endoribonuclease XendoU | Q8JFY9 |
| PF09636 | XkdW | XkdW protein | P54342 |
| PF09722 | Xre_MbcA_ParS_C | Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain | Q88K58 |
| PF09815 | XK-related | XK-related protein | Q5GH54 |
| PF10779 | XhlA | Haemolysin XhlA | |
| PF11952 | XTBD | XRN-Two Binding Domain, XTBD | Q21738 |
| PF12529 | Xylo_C | Xylosyltransferase C terminal | Q86Y38 |
| PF12813 | XPG_I_2 | XPG domain containing | |
| PF13478 | XdhC_C | XdhC Rossmann domain | Q9KBF4 |
| PF14440 | XOO_2897-deam | Xanthomonas XOO_2897-like deaminase | |
| PF17846 | XRN_M | Xrn1 helical domain | G0S058 |
| PF18245 | XRN1_DBM | 5-3 exonuclease XRN1 DCP1-binding motif | E1JJR3 |
| PF18332 | XRN1_D1 | Exoribonuclease Xrn1 D1 domain | P22147 |
| PF18334 | XRN1_D2_D3 | Exoribonuclease Xrn1 D2/D3 domain | Q6CJ09 |
| PF18458 | XPB_DRD | Xeroderma pigmentosum group B helicase damage recognition domain | O29889 |
| PF18608 | XAF1_C | XIAP-associated factor 1 C-terminal domain | Q6GPH4 |
| PF19977 | xRRM | xRRM domain | O13795 |
| PF20410 | X-Tfes_XVIPCD | X-Tfes, XVIPCD | B2FJG3 |
| PF20432 | Xre-like-HTH | Antitoxin Xre-like helix-turn-helix domain | Q88K58 |
| PF20817 | XopL_C | Type III effector Xcv3220, C-terminal domain | |
| PF21041 | XMAP215_CLASP_TOG | XMAP215/Dis1/CLASP, TOG domain | |
| PF21924 | XRCC4_CC | XRCC4 coiled-coil | |
| PF21925 | XRCC4_C | XRCC4 C-terminal region | |
| PF21928 | XLF_CC | XLF protein coiled-coil region | |
| PF22058 | X25_BaPul_like | Pullulanase X25 domain | |
| PF22139 | XPD_arch | DNA repair helicase XPD, arch domain | |
| PF23124 | Xre_MbcA_ParS-like_N | Antitoxin Xre/MbcA/ParS-like, N-terminal | |
| PF23125 | Xre-MbcA-ParS_M | Antitoxin Xre/MbcA/ParS-like, middle domain | |
| PF24482 | XPB_C | XPB-like, C-terminal domain | |