Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity)
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| ubiquitin | PF00240 | 98 - 156 | 1.1e-09 | Ubiquitin family |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AccB7I | CCANNNNNTGG | 1 cut(s) | 62 |
| AccI | GTMKAC | 1 cut(s) | 300 |
| AclWI | GGATC | 1 cut(s) | 217 |
| AcoI | YGGCCR | 1 cut(s) | 233 |
| AcsI | RAATTY | 1 cut(s) | 38 |
| AcvI | CACGTG | 1 cut(s) | 123 |
| AdeI | CACNNNGTG | 1 cut(s) | 220 |
| AfaI | GTAC | 2 cut(s) | 77, 275 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 62 |
| AgsI | TTSAA | 4 cut(s) | 38, 349, 362, 489 |
| AjnI | CCWGG | 2 cut(s) | 181, 376 |
| AluBI | AGCT | 1 cut(s) | 155 |
| AluI | AGCT | 1 cut(s) | 155 |
| AlwI | GGATC | 1 cut(s) | 217 |
| AoxI | GGCC | 3 cut(s) | 195, 233, 374 |
| ApaI | GGGCCC | 1 cut(s) | 199 |
| ApoI | RAATTY | 1 cut(s) | 38 |
| AspS9I | GGNCC | 3 cut(s) | 195, 196, 374 |
| BaeGI | GKGCMC | 1 cut(s) | 199 |
| BalI | TGGCCA | 1 cut(s) | 235 |
| BanII | GRGCYC | 1 cut(s) | 199 |
| BbrPI | CACGTG | 1 cut(s) | 123 |
| BbsI | GAAGAC | 1 cut(s) | 369 |
| BccI | CCATC | 1 cut(s) | 395 |
| BciT130I | CCWGG | 2 cut(s) | 183, 378 |
| BfaI | CTAG | 2 cut(s) | 278, 517 |
| Bme1390I | CCNGG | 2 cut(s) | 183, 378 |
| BmgT120I | GGNCC | 3 cut(s) | 195, 196, 374 |
| BmiI | GGNNCC | 2 cut(s) | 197, 198 |
| BmrFI | CCNGG | 2 cut(s) | 183, 378 |
| BmrI | ACTGGG | 1 cut(s) | 50 |
| BmuI | ACTGGG | 1 cut(s) | 50 |
| BpiI | GAAGAC | 1 cut(s) | 369 |
| BpmI | CTGGAG | 1 cut(s) | 204 |
| Bpu10I | CCTNAGC | 1 cut(s) | 201 |
| BpuEI | CTTGAG | 1 cut(s) | 313 |
| BsaAI | YACGTR | 1 cut(s) | 123 |
| BsaJI | CCNNGG | 2 cut(s) | 227, 377 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 62 |
| Bse1I | ACTGG | 1 cut(s) | 56 |
| Bse3DI | GCAATG | 1 cut(s) | 133 |
| BseBI | CCWGG | 2 cut(s) | 183, 378 |
| BseDI | CCNNGG | 2 cut(s) | 227, 377 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 62 |
| BseMI | GCAATG | 1 cut(s) | 133 |
| BseMII | CTCAG | 1 cut(s) | 192 |
| BseNI | ACTGG | 1 cut(s) | 56 |
| BseRI | GAGGAG | 1 cut(s) | 284 |
| BseSI | GKGCMC | 1 cut(s) | 199 |
| BshFI | GGCC | 3 cut(s) | 197, 235, 376 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 62 |
| BsnI | GGCC | 3 cut(s) | 197, 235, 376 |
| Bsp120I | GGGCCC | 1 cut(s) | 195 |
| Bsp1286I | GDGCHC | 1 cut(s) | 199 |
| Bsp143I | GATC | 1 cut(s) | 222 |
| Bsp19I | CCATGG | 1 cut(s) | 227 |
| BspANI | GGCC | 3 cut(s) | 197, 235, 376 |
| BspCNI | CTCAG | 1 cut(s) | 193 |
| BspHI | TCATGA | 1 cut(s) | 265 |
| BspLI | GGNNCC | 2 cut(s) | 197, 198 |
| BspPI | GGATC | 1 cut(s) | 217 |
| BsrDI | GCAATG | 1 cut(s) | 133 |
| BsrI | ACTGG | 1 cut(s) | 56 |
| BssECI | CCNNGG | 2 cut(s) | 227, 377 |
| BssMI | GATC | 1 cut(s) | 222 |
| BssT1I | CCWWGG | 1 cut(s) | 227 |
| Bst2UI | CCWGG | 2 cut(s) | 183, 378 |
| Bst4CI | ACNGT | 1 cut(s) | 289 |
| BstBAI | YACGTR | 1 cut(s) | 123 |
| BstC8I | GCNNGC | 1 cut(s) | 435 |
| BstDEI | CTNAG | 2 cut(s) | 201, 462 |
| BstDSI | CCRYGG | 1 cut(s) | 227 |
| BstKTI | GATC | 1 cut(s) | 225 |
| BstMBI | GATC | 1 cut(s) | 222 |
| BstNI | CCWGG | 2 cut(s) | 183, 378 |
| BstSCI | CCNGG | 2 cut(s) | 181, 376 |
| BstSLI | GKGCMC | 1 cut(s) | 199 |
| BstV2I | GAAGAC | 1 cut(s) | 369 |
| BsuRI | GGCC | 3 cut(s) | 197, 235, 376 |
| BtgI | CCRYGG | 1 cut(s) | 227 |
| BtsIMutI | CAGTG | 1 cut(s) | 285 |
| Cac8I | GCNNGC | 1 cut(s) | 435 |
| CciI | TCATGA | 1 cut(s) | 265 |
| Cfr13I | GGNCC | 3 cut(s) | 195, 196, 374 |
| Csp6I | GTAC | 2 cut(s) | 76, 274 |
| CviAII | CATG | 4 cut(s) | 62, 86, 228, 266 |
| CviJI | RGCY | 8 cut(s) | 106, 155, 197, 235, 376, 433, 499, 511 |
| CviKI_1 | RGCY | 8 cut(s) | 106, 155, 197, 235, 376, 433, 499, 511 |
| CviQI | GTAC | 2 cut(s) | 76, 274 |
| DdeI | CTNAG | 2 cut(s) | 201, 462 |
| DpnI | GATC | 1 cut(s) | 224 |
| DpnII | GATC | 1 cut(s) | 222 |
| DraIII | CACNNNGTG | 1 cut(s) | 220 |
| EaeI | YGGCCR | 1 cut(s) | 233 |
| Eco130I | CCWWGG | 1 cut(s) | 227 |
| Eco24I | GRGCYC | 1 cut(s) | 199 |
| Eco32I | GATATC | 1 cut(s) | 283 |
| Eco72I | CACGTG | 1 cut(s) | 123 |
| EcoO109I | RGGNCCY | 2 cut(s) | 196, 374 |
| EcoRI | GAATTC | 1 cut(s) | 38 |
| EcoRII | CCWGG | 2 cut(s) | 181, 376 |
| EcoRV | GATATC | 1 cut(s) | 283 |
| EcoT14I | CCWWGG | 1 cut(s) | 227 |
| EcoT38I | GRGCYC | 1 cut(s) | 199 |
| ErhI | CCWWGG | 1 cut(s) | 227 |
| FaeI | CATG | 4 cut(s) | 65, 89, 231, 269 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 483, 515 |
| FatI | CATG | 4 cut(s) | 61, 85, 227, 265 |
| FblI | GTMKAC | 1 cut(s) | 300 |
| FriOI | GRGCYC | 1 cut(s) | 199 |
| FspBI | CTAG | 2 cut(s) | 278, 517 |
| GsuI | CTGGAG | 1 cut(s) | 204 |
| HaeIII | GGCC | 3 cut(s) | 197, 235, 376 |
| Hin1II | CATG | 4 cut(s) | 65, 89, 231, 269 |
| HinfI | GANTC | 1 cut(s) | 447 |
| Hpy166II | GTNNAC | 2 cut(s) | 76, 301 |
| Hpy188I | TCNGA | 1 cut(s) | 508 |
| Hpy188III | TCNNGA | 2 cut(s) | 134, 266 |
| Hpy8I | GTNNAC | 2 cut(s) | 76, 301 |
| HpyCH4III | ACNGT | 1 cut(s) | 289 |
| HpyCH4IV | ACGT | 2 cut(s) | 31, 122 |
| HpyCH4V | TGCA | 3 cut(s) | 8, 126, 437 |
| HpyF3I | CTNAG | 2 cut(s) | 201, 462 |
| HpySE526I | ACGT | 2 cut(s) | 31, 122 |
| Hsp92II | CATG | 4 cut(s) | 65, 89, 231, 269 |
| Kzo9I | GATC | 1 cut(s) | 222 |
| LpnPI | CCDG | 6 cut(s) | 69, 168, 195, 213, 363, 390 |
| MaeI | CTAG | 2 cut(s) | 278, 517 |
| MaeII | ACGT | 2 cut(s) | 31, 122 |
| MaeIII | GTNAC | 1 cut(s) | 118 |
| MalI | GATC | 1 cut(s) | 224 |
| MboI | GATC | 1 cut(s) | 222 |
| MboII | GAAGA | 2 cut(s) | 374, 428 |
| MfeI | CAATTG | 1 cut(s) | 344 |
| MhlI | GDGCHC | 1 cut(s) | 199 |
| MlsI | TGGCCA | 1 cut(s) | 235 |
| MluCI | AATT | 4 cut(s) | 38, 243, 344, 357 |
| MluNI | TGGCCA | 1 cut(s) | 235 |
| MnlI | CCTC | 1 cut(s) | 262 |
| Mox20I | TGGCCA | 1 cut(s) | 235 |
| MscI | TGGCCA | 1 cut(s) | 235 |
| MseI | TTAA | 2 cut(s) | 315, 339 |
| MslI | CAYNNNNRTG | 1 cut(s) | 399 |
| Msp20I | TGGCCA | 1 cut(s) | 235 |
| MspR9I | CCNGG | 2 cut(s) | 183, 378 |
| MunI | CAATTG | 1 cut(s) | 344 |
| MvaI | CCWGG | 2 cut(s) | 183, 378 |
| NcoI | CCATGG | 1 cut(s) | 227 |
| NdeII | GATC | 1 cut(s) | 222 |
| NlaIII | CATG | 4 cut(s) | 65, 89, 231, 269 |
| NlaIV | GGNNCC | 2 cut(s) | 197, 198 |
| NmuCI | GTSAC | 1 cut(s) | 118 |
| PagI | TCATGA | 1 cut(s) | 265 |
| PfeI | GAWTC | 1 cut(s) | 447 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 62 |
| PfoI | TCCNGGA | 1 cut(s) | 181 |
| PmaCI | CACGTG | 1 cut(s) | 123 |
| PmlI | CACGTG | 1 cut(s) | 123 |
| Ppu21I | YACGTR | 1 cut(s) | 123 |
| Psp6I | CCWGG | 2 cut(s) | 181, 376 |
| PspCI | CACGTG | 1 cut(s) | 123 |
| PspGI | CCWGG | 2 cut(s) | 181, 376 |
| PspN4I | GGNNCC | 2 cut(s) | 197, 198 |
| PspOMI | GGGCCC | 1 cut(s) | 195 |
| PspPI | GGNCC | 3 cut(s) | 195, 196, 374 |
| RsaI | GTAC | 2 cut(s) | 77, 275 |
| RsaNI | GTAC | 2 cut(s) | 76, 274 |
| RseI | CAYNNNNRTG | 1 cut(s) | 399 |
| SaqAI | TTAA | 2 cut(s) | 315, 339 |
| Sau3AI | GATC | 1 cut(s) | 222 |
| Sau96I | GGNCC | 3 cut(s) | 195, 196, 374 |
| ScrFI | CCNGG | 2 cut(s) | 183, 378 |
| SduI | GDGCHC | 1 cut(s) | 199 |
| SetI | ASST | 7 cut(s) | 19, 34, 125, 157, 279, 321, 325 |
| SmiMI | CAYNNNNRTG | 1 cut(s) | 399 |
| SmlI | CTYRAG | 1 cut(s) | 328 |
| SmoI | CTYRAG | 1 cut(s) | 328 |
| Sse9I | AATT | 4 cut(s) | 38, 243, 344, 357 |
| SspI | AATATT | 1 cut(s) | 165 |
| SspMI | CTAG | 2 cut(s) | 278, 517 |
| StyD4I | CCNGG | 2 cut(s) | 181, 376 |
| StyI | CCWWGG | 1 cut(s) | 227 |
| TaaI | ACNGT | 1 cut(s) | 289 |
| TaiI | ACGT | 2 cut(s) | 34, 125 |
| TasI | AATT | 4 cut(s) | 38, 243, 344, 357 |
| TatI | WGTACW | 1 cut(s) | 75 |
| TfiI | GAWTC | 1 cut(s) | 447 |
| Tru1I | TTAA | 2 cut(s) | 315, 339 |
| Tru9I | TTAA | 2 cut(s) | 315, 339 |
| TscAI | CASTG | 1 cut(s) | 292 |
| TseFI | GTSAC | 1 cut(s) | 118 |
| Tsp45I | GTSAC | 1 cut(s) | 118 |
| TspDTI | ATGAA | 3 cut(s) | 10, 50, 402 |
| TspRI | CASTG | 1 cut(s) | 292 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 62 |
| XapI | RAATTY | 1 cut(s) | 38 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 59 |
| XmiI | GTMKAC | 1 cut(s) | 300 |
| XspI | CTAG | 2 cut(s) | 278, 517 |