| PF01398 | JAB | JAB1/Mov34/MPN/PAD-1 ubiquitin protease | O00487 |
| PF01419 | Jacalin | Jacalin-like lectin domain | Q306J3 |
| PF02099 | Josephin | Josephin | Q8TAC2 |
| PF02373 | JmjC | JmjC domain, hydroxylase | O75151 |
| PF02375 | JmjN | jmjN domain | Q92833 |
| PF03957 | Jun | Jun-like transcription factor | |
| PF05439 | JTB | Jumping translocation breakpoint protein (JTB) | O76095 |
| PF05571 | JAMP | JNK1/MAPK8-associated membrane protein | |
| PF06585 | JHBP | Haemolymph juvenile hormone binding protein (JHBP) | B5ABT1 |
| PF07086 | Jagunal | Jagunal, ER re-organisation during oogenesis | Q8N5M9 |
| PF08007 | JmjC_2 | JmjC domain | Q9H6W3 |
| PF09425 | Jas_motif | Jas motif | Q93ZM9 |
| PF09983 | JetD_C | Wadjet protein JetD, C-terminal | A0A0H2ZM47 |
| PF14804 | Jag_N | Jag N-terminus | D0VX24 |
| PF14901 | Jiv90 | Cleavage inducing molecular chaperone | |
| PF15038 | Jiraiya | Jiraiya | |
| PF15261 | JHY | Jhy protein | |
| PF15312 | JSRP | Junctional sarcoplasmic reticulum protein | |
| PF15351 | JCAD | Junctional protein associated with coronary artery disease | |
| PF15392 | Joubert | Joubert syndrome-associated | |
| PF15871 | JMY | Junction-mediating and -regulatory protein | |
| PF16034 | JAKMIP_CC3 | JAKMIP CC3 domain | |
| PF16471 | JIP_LZII | JNK-interacting protein leucine zipper II | Q9ESN9 |
| PF16668 | JLPA | Adhesin from Campylobacter | A0A0H3P9U7 |
| PF17054 | JUPITER | Microtubule-Associated protein Jupiter | |
| PF17811 | JHD | Jumonji helical domain | O75151 |
| PF17887 | Jak1_Phl | Jak1 pleckstrin homology-like domain | B1ASP2 |
| PF18982 | JetA | Wadjet protein JetA | |
| PF21795 | JAG1-like_EGF2 | Protein jagged-1-like, atypical EGF2 | |
| PF22794 | jr-ZPR1 | ZPR1 jelly-roll domain | |
| PF23575 | JAG1 | Protein jagged-1-like, predicted ferredoxin-like domain | |