PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325114519 227 CNRLMKKYKKDQKEALRVCFTTVRVYCANAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFKDTGDFLV-ING 305
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFiINK 80

                         90       100
                 ....*....|....*....|
gi 325114519 306 QPDGFVLGQALKFIDVLLEQ 325
Cdd:cd10462   81 IPDTFLCSQAIKFIDLILQT 100

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 325114519  134 EEEAQRRAYELQKKLREDRLEREKREAIEREKLRLAQTKAMLE-QNAKLEEEQRKRQLAQLQKEKEMPE 201
Cdd:pfam17380 482 EKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEErQKAIYEEERRREAEEERRKQQEMEE 550

PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325114519 227 CNRLMKKYKKDQKEALRVCFTTVRVYCANAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFKDTGDFLV-ING 305
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFiINK 80

                         90       100
                 ....*....|....*....|
gi 325114519 306 QPDGFVLGQALKFIDVLLEQ 325
Cdd:cd10462   81 IPDTFLCSQAIKFIDLILQT 100

PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain. This domain is also found on other proteins linked to the ubiquitin-proteasome system.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325114519  239 KEALRVCFTTVRVYCANAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFK--DTGDFLVI 303
Cdd:pfam09409   1 KEKVKEALETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFEkeDEEEFLLL 67

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 325114519   66 INMEQVDQLVDFGFPRLRAEKALFhvrqhSADGAIEAAVEWL 107
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALR-----ATGNNVERAAEYL 37

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 325114519    69 EQVDQLVDFGFPRLRAEKALfhvrqHSADGAIEAAVEWL 107
Cdd:smart00165   3 EKIDQLLEMGFSREEALKAL-----RAANGNVERAAEYL 36

PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325114519 227 CNRLMKKYKKDQKEALRVCFTTVRVYCANAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFKDTGDFLV-ING 305
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFiINK 80

                         90       100
                 ....*....|....*....|
gi 325114519 306 QPDGFVLGQALKFIDVLLEQ 325
Cdd:cd10462   81 IPDTFLCSQAIKFIDLILQT 100

PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325114519 240 EALRVCFTTVRVYCANAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFKDTGD----FLVINGQPDGFVLGQA 315
Cdd:cd09212   11 EAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEETEsgesFLVLPDDADVDLLKDA 90

                 ....*
gi 325114519 316 LKFID 320
Cdd:cd09212   91 KAALE 95

PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. This family contains only plant UBA domain-containing proteins.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325114519 229 RLMKKYKKDQKEALRVCFTTVRVYCANAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFK--DTGDFLVI 303
Cdd:cd10461    2 VDLKKAHKDDPDAVKTAFQTLLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFErdEGDEALVL 78

PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. WLM domains are found mostly in plant proteins, belonging to the Zincin-like superfamily of Zn-dependent peptidases that are linked to the ubiquitin signaling pathway through its fusion with the ubiquitin-binding PUB, ubiquitin-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 325114519 240 EALRVCFTTVRvycaNAKDHPLEEKFLKIRKENNAFKSRVLPFEGALDLLDVCGFKDTGDFlvingQPDGFVLG 313
Cdd:cd10463   16 SALQTLFKILG----NAIEHPNEDKFRRLRKSNPAFQRRVARFPGAVELLLAAGFAEEGVS-----GPDTYLLL 80

UBA1 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 325114519  67 NMEQVDQLVDFGFPRLRAEKALFHVRQHSAdgaiEAAVEWLEAHAEDDDVD 117
Cdd:cd14385    1 NAEALAQLLGMGFPEVRCKKALLATGNSDA----EAAMNWLFEHMDDPDID 47

UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins; This family includes some uncharacterized hypothetical proteins found in plants. Although their biological function remain unclear, all family members contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal PUB domain. UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 325114519  66 INMEQVDQLVDFGFPRLRAEKALFHvrqhSADGAIEAAVEWLEAHAEDDDVD 117
Cdd:cd14290    2 VNADLLKELEAMGFPRARAVRALHH----TGNTSVEAAVNWIVEHENDPDID 49

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 325114519  134 EEEAQRRAYELQKKLREDRLEREKREAIEREKLRLAQTKAMLE-QNAKLEEEQRKRQLAQLQKEKEMPE 201
Cdd:pfam17380 482 EKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEErQKAIYEEERRREAEEERRKQQEMEE 550

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins; UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5. It has similar domain architecture, but functions differently from USP5 in cellular deubiquitination processes. It exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin in a non-activation manner. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 325114519  71 VDQLVDFGFPRLRAEKALFHvrqhSADGAIEAAVEWLEAHAEDDD 115
Cdd:cd14294    4 VSQLAEMGFPLEACRKAVYH----TNNSGLEAAMNWIMEHMDDPD 44

UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 325114519  68 MEQVDQLVDFGFPRLRAEKALfhvrqHSADGAIEAAVEWLEAHA 111
Cdd:cd14297    1 EDLVKQLVDMGFTEAQARKAL-----RKTNNNVERAVDWLFEGP 39

MAEBL; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325114519  134 EEEAQRRAYELQKKLREDRLEREKREAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEMPEEDDSTEEGAAAR 213
Cdd:PTZ00121 1670 AEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEA 1749

                          90       100       110
                  ....*....|....*....|....*....|.
gi 325114519  214 LKKMSGKEKVAYWCNRLMKKYKKDQKEALRV 244
Cdd:PTZ00121 1750 KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAV 1780

UBA domain found in eukaryotic E3 ubiquitin-protein ligase HUWE1 and similar proteins; HUWE1, also called ARF-binding protein 1 (ARF-BP1), HECT, UBA and WWE domain-containing protein 1, homologous to E6AP carboxyl terminus homologs protein 9 (HectH9), large structure of UREB1 (LASU1), Mcl-1 ubiquitin ligase E3 (Mule), upstream regulatory element-binding protein 1 (URE-B1), or URE-binding protein 1, may function as a ubiquitin-protein ligase that involves in the ubiquitination cascade that targets specific substrate proteins in proteolysis. It can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase and modulates base excision repair (BER). HUWE1 also acts as a critical mediator of both the p53-independent and p53-dependent tumor suppressor functions of ARF tumor suppressor in p53 regulation. Moreover, HUWE1 is both required and sufficient for the polyubiquitination of Mcl-1, an anti-apoptotic Bcl-2 family member involving in DNA damage-induced apoptosis. Furthermore, HUWE1 plays an important role in the regulation of Cdc6 stability after DNA damage. In addition, HUWE1 works as a partner of N-Myc oncoprotein in neural cells. It ubiquitinates N-Myc and primes it for proteasomal-mediated degradation. HUWE1 contains a ubiquitin-associated (UBA) domain, a WWE domain, and a Bcl-2 homology region 3 (BH3) domain at the N-terminus and a HECT domain at the C-terminus. WWE domain plays a role in the regulation of specific protein-protein interactions in a ubiquitin conjugation system. BH3 domain is responsible for the specific binding to Mcl-1. HECT domain involves in the inhibition of the transcriptional activity of p53 via a ubiquitin-dependent degradation pathway. It also controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 325114519  66 INMEQVDQLVDFGFPRLRAEKALFHVrqhsadGAIEAAVEWLEAH 110
Cdd:cd14288    1 VNEAHLQQLMDMGFTREHALEALLHT------STLEQATEYLLTH 39

UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 325114519  69 EQVDQLVDFGFPRLRAEKALfhvrqHSADGAIEAAVEWL 107
Cdd:cd14307    2 EAVASLLEMGIPREVAIEAL-----RETNGDVEAAANYI 35

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325114519  134 EEEAQRRAYELqkKLREDRLEREKREAIEREKLRLAQTKaMLEQNAKLEEEQRKRQLAQLQKEKEMPEeddsTEEGAAAR 213
Cdd:pfam15709 379 ELEQQRRFEEI--RLRKQRLEEERQRQEEEERKQRLQLQ-AAQERARQQQEEFRRKLQELQRKKQQEE----AERAEAEK 451

                          90       100       110
                  ....*....|....*....|....*....|
gi 325114519  214 LKKMSGKEKVAYWCNRLMKKYKKDQKEALR 243
Cdd:pfam15709 452 QRQKELEMQLAEEQKRLMEMAEEERLEYQR 481

UBA1 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins; KPC2, also called ubiquitin-associated domain-containing protein 1 (UBAC1), or glialblastoma cell differentiation-related protein 1, is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains a ubiquitin-like (UBL) domain and two ubiquitin-associated (UBA) domains. This model corresponds to the UBA1 domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 325114519  66 INMEQVDQLVDFGFPRLRAEKALFHVRQHsadgaIEAAVEWLEAHA 111
Cdd:cd14303    1 VDPEALKQLTEMGFPEARATKALLLNRMS-----PTQAMEWLLEHE 41