| PF00095 | WAP | WAP-type (Whey Acidic Protein) 'four-disulfide core' | P19957 |
| PF00110 | wnt | wnt family | Q9H1J5 |
| PF00397 | WW | WW domain | Q13526 |
| PF00400 | WD40 | WD domain, G-beta repeat | P62873 |
| PF00458 | WHEP-TRS | WHEP-TRS domain | P12081 |
| PF00568 | WH1 | WH1 domain | Q8N8S7 |
| PF01822 | WSC | WSC domain | Q96MU8 |
| PF02019 | WIF | WIF domain | Q7JQT0 |
| PF02020 | W2 | eIF4-gamma/eIF5/eIF2-epsilon | Q13144 |
| PF02165 | WT1 | Wilm's tumour protein | |
| PF02205 | WH2 | WH2 motif | Q91YD9 |
| PF02206 | WSN | Domain of unknown function | |
| PF02467 | Whib | Transcription factor WhiB | A0A5P2AC98 |
| PF02706 | Wzz | Chain length determinant protein | Q9X4B9 |
| PF02825 | WWE | WWE domain | Q7Z2W4 |
| PF03007 | WS_DGAT_cat | Wax ester synthase/diacylglycerol acyltransferase catalytic domain | Q8GGG1 |
| PF03106 | WRKY | WRKY DNA -binding domain | Q9C5T4 |
| PF03303 | WTF | WTF protein | |
| PF03716 | WCCH | WCCH motif | |
| PF03832 | WSK | WSK motif | P24588 |
| PF04932 | Wzy_C | O-Antigen ligase | Q1LJU1 |
| PF05406 | WGR | WGR domain | P09874 |
| PF05562 | WCOR413 | Cold acclimation protein WCOR413 | |
| PF05701 | WEMBL | Weak chloroplast movement under blue light | |
| PF06013 | WXG100 | Proteins of 100 residues with WXG | P9WNK5 |
| PF06030 | WxLIP_PGBD | WxL Interacting Protein, peptidoglycan binding domain | |
| PF06176 | WaaY | Lipopolysaccharide core biosynthesis protein (WaaY) | |
| PF06664 | WLS-like_TM | Wntless-like, transmembrane domain | Q5T9L3 |
| PF06899 | WzyE | WzyE protein, O-antigen assembly polymerase | |
| PF06974 | WS_DGAT_C | WS/DGAT C-terminal domain | Q8GGG1 |
| PF07107 | WI12 | Wound-induced protein WI12 | |
| PF07483 | W_rich_C | Tryptophan-rich Synechocystis species C-terminal domain | |
| PF07507 | WavE | WavE lipopolysaccharide synthesis | |
| PF07814 | WAPL | Wings apart-like protein regulation of heterochromatin | Q7Z5K2 |
| PF08186 | Wound_ind | Wound-inducible basic protein family | |
| PF08325 | WLM | WLM domain | O94580 |
| PF08488 | WAK | Wall-associated kinase | |
| PF08528 | Whi5 | Whi5 like | |
| PF08536 | Whirly | Whirly transcription factor | Q66GR6 |
| PF08608 | Wyosine_form | Wyosine base formation | Q57705 |
| PF08879 | WRC | WRC | |
| PF08889 | WbqC | WbqC-like protein family | |
| PF09429 | Wbp11 | WW domain binding protein 11 | Q9Y2W2 |
| PF09688 | Wx5_PLAF3D7 | Protein of unknown function (Wx5_PLAF3D7) | |
| PF10180 | WKF | WKF domain | |
| PF10206 | WRW | Mitochondrial F1F0-ATP synthase, subunit f | Q28851 |
| PF10273 | WGG | Pre-rRNA-processing protein TSR2 | Q06672 |
| PF10298 | WhiA_N | WhiA N-terminal LAGLIDADG-like domain | A0A5P1ZKC3 |
| PF10357 | WH_KIN17 | KIN17 WH-like domain | O60870 |
| PF10440 | WIYLD | Ubiquitin-binding WIYLD domain | Q8W595 |
| PF10537 | WAC_Acf1_DNA_bd | ATP-utilising chromatin assembly and remodelling N-terminal | |
| PF10902 | WYL_2 | WYL_2, Sm-like SH3 beta-barrel fold | |
| PF11669 | WBP-1 | WW domain-binding protein 1 | |
| PF11797 | WxLIP_HBD | WxL Interacting Protein, host binding domain | |
| PF11846 | Wzy_C_2 | Virulence factor membrane-bound polymerase, C-terminal | |
| PF11945 | WASH_WAHD | WAHD domain of WASH complex | |
| PF12264 | Waikav_capsid_1 | Waikavirus capsid protein 1 | |
| PF12589 | WBS_methylT | Methyltransferase involved in Williams-Beuren syndrome | O43709 |
| PF12779 | WXXGXW | WXXGXW repeat (2 copies) | |
| PF13280 | WYL | WYL domain | Q9A999 |
| PF13731 | WxL | WxL domain surface cell wall-binding | |
| PF13943 | WPP | WPP domain | I7JSB1 |
| PF14043 | WVELL | WVELL protein | |
| PF14077 | WD40_alt | Alternative WD40 repeat motif | Q9BV38 |
| PF14380 | WAK_assoc | Wall-associated receptor kinase C-terminal | |
| PF14414 | WHH | A nuclease of the HNH/ENDO VII superfamily with conserved WHH | Q87PI5 |
| PF14524 | Wzt_C | Wzt C-terminal domain | O67181 |
| PF14744 | WASH-7_mid | WASH complex subunit 7 | |
| PF14745 | WASH-4_N | WASH complex subunit 4, N-terminal | |
| PF14746 | WASH-7_C | WASH complex subunit 7, C-terminal | |
| PF14903 | WG_beta_rep | WG containing repeat | |
| PF15017 | WRNPLPNID | Putative WW-binding domain and destruction box | Q9ULX3 |
| PF15164 | WBS28 | Williams-Beuren syndrome chromosomal region 28 protein homologue | |
| PF15390 | WDCP | WD repeat and coiled-coil-containing protein family | |
| PF15612 | WHIM1 | WSTF, HB1, Itc1p, MBD9 motif 1 | P43596 |
| PF15613 | WSD | Williams-Beuren syndrome DDT (WSD), D-TOX E motif | |
| PF15920 | WHAMM-JMY_N | N-terminal of Junction-mediating and WASP homolog-associated | |
| PF16300 | WD40_4 | Type of WD40 repeat | Q9ULV4 |
| PF16623 | WW_FCH_linker | Unstructured linker region between on GAS7 protein | Q60780 |
| PF16997 | Wap1 | Wap1 domain | Q75E93 |
| PF17005 | WD40_like | WD40-like domain | |
| PF17098 | Wtap | WTAP/Mum2p family | Q15007 |
| PF17890 | WW_like | Peptidoglycan hydrolase LytB WW-like domain | P59206 |
| PF18412 | Wza_C | Outer-membrane lipoprotein Wza C-terminal domain | Q9X4B7 |
| PF18488 | WYL_3 | WYL domain | D0NIN5 |
| PF18507 | WW_1 | WW domain | P46995 |
| PF18588 | WcbI | Polysaccharide biosynthesis enzyme WcbI | Q63R74 |
| PF18972 | Wheel | Cns1/TTC4 Wheel domain | P33313 |
| PF19056 | WD40_2 | WD40 repeated domain | |
| PF19306 | WH_Lhr | Large helicase-related protein, winged helix domain | |
| PF19913 | WCOB | Wolframin C-terminal OB-fold domain | |
| PF19914 | WEF-hand | Wolframin EF-hand domain | |
| PF20023 | WSLR | Wolframin Sel1-like repeat | |
| PF20053 | WC-rich | Wolframin cysteine-rich domain | |
| PF20493 | WD-like_fungi | Fungal WD-like | |
| PF20625 | WW_USP8 | USP8 WW domain | |
| PF20853 | WKTW_rpt | WKTW repeat | |
| PF21030 | WDR93 | WD repeat-containing protein 93 | |
| PF21031 | WDR54 | WDR54 | |
| PF21374 | WsaF_N | WsaF, N-terminal domain | |
| PF21662 | WipA_N | WipA, alpha-helical hairpin | |
| PF21663 | WipA_Phos | WipA-like, phosphatase domain | |
| PF21883 | WLS_GOLD | Wntless, GOLD domain | |
| PF22005 | WWE_1 | Parp14 WWE domain | |
| PF22532 | WIV_dom | Nonstructural protein, WIV domain | |
| PF22537 | WbmS-like | Polysaccharide deacetylase | |
| PF22772 | WsaF_C | WsaF, C-terminal domain | |
| PF22814 | WelO5 | Carrier-protein-independent halogenase WelO5 | |
| PF22977 | WHD | Winged helix domain, variant | |
| PF22982 | WHD_HRQ1 | ATP-dependent helicase HRQ1, winged helix domain | |
| PF23123 | WDR72_alpha-sol | WDR72, alpha-solenoid domain | |
| PF23159 | WH_Rok | Repressor Rok winged helix domain | |
| PF23184 | WD40_CFAP43 | CFAP43, WD40 domain | |
| PF23191 | WH_MCM3_C | MCM3-like, winged helix domain | |
| PF23215 | WD_LRWD1 | Leucine-rich repeat and WD repeat-containing protein 1, WD domain | |
| PF23216 | WH_CYT4 | Mitochondrial protein cyt-4, winged helix | |
| PF23234 | WH4_Lhr | Large helicase-related protein, winged-helix domain | |
| PF23235 | WH3_Lhr | Large helicase-related protein, winged-helix domain | |
| PF23236 | WH2_Lhr | Large helicase-related protein, winged-helix domain | |
| PF23282 | WHD_ROQ1 | Disease resistance protein Roq1-like, winged-helix domain | |
| PF23342 | WDR90_beta-prop_4th | WDR90, 4th beta-propeller | |
| PF23405 | WD40_APC4_C-half | APC4, WD40 domain C-terminal half | |
| PF23407 | WD40_Apc4_C_fungal | Apc4 WD40 domain C-terminal half, fungal | |
| PF23419 | WD40_RFWD3 | E3 ubiquitin-protein ligase RFWD3 WD40 domain | |
| PF23463 | WWE_2 | WWE domain | |
| PF23464 | WWE_3 | WWE domain | |
| PF23466 | WWE_4 | WWE domain | |
| PF23467 | WWE_5 | WWE domain | |
| PF23517 | WW_TCERG1 | TCERG1 WW domain | |
| PF23518 | WW_2 | WW domain | |
| PF23559 | WH_DRP | Disease resistance protein Winged helix domain | |
| PF23582 | WH_RGF3 | RGF3 winged helix domain | |
| PF23589 | WH_AprA | AprA winged helix domain | |
| PF23607 | WZC_N | Tyrosine-protein kinase Wzc, N-terminal domain | |
| PF23669 | WH_MCM2 | DNA replication licensing factor MCM2-like, winged-helix domain | |
| PF23704 | WH_GTF3C1_N | General transcription factor 3C polypeptide 1, winged-helix domain | |
| PF23713 | WH_Egal | Egalitarian winged helix domain | |
| PF24356 | WH_PARP12 | PARP12 winged helix domain | |
| PF24408 | wHTH-Calcineurin_assc | wHTH-Calcineurin_assc | |
| PF24409 | wHTH-PRTase_assc | wHTH-PRTase associated | |
| PF24410 | wHTH-HSP90_Na-assoc | wHTH-Hsp90_Na associated | |
| PF24413 | W02B3_4_N | W02B3.4-like, N-terminal domain | |
| PF24716 | WapI | Immunity protein WapI-like family | |
| PF24780 | WD40_MABP1-WDR62_1st | MABP1/WDR62 first WD40 domain | |
| PF24782 | WD40_MABP1-WDR62_2nd | MABP1/WDR62 second WD40 domain | |
| PF24795 | WDR62-MABP1_CC | WRD62/MABP1 coiled-coil | |
| PF24796 | WDR55 | WDR55 | |
| PF24807 | WD40_CDC20-Fz | CDC20/Fizzy WD40 domain | |
| PF24812 | wHTH_TTC3 | TTC3-like, winged helix turn helix domain | |
| PF24814 | WD40_Prp19 | Prp19 WD40 domain | |
| PF24817 | WD40_WDHD1_1st | WDHD1 first WD40 domain | |