F-box domain found in F-box only protein 7 (FBXO7) and similar proteins; FBXO7, also called FBX7, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It recognizes BIRC2 and DLGAP5. FBXO7 plays a role downstream of PINK1 in the clearance of damaged mitochondria via selective autophagy (mitophagy) by targeting PRKN to dysfunctional depolarized mitochondria. It promotes MFN1 ubiquitination. FBXO7 acts as a cell cycle regulator by enhancing cyclin D/cyclin-dependent kinase 6 (Cdk6) complex formation and stabilizing levels of p27, a cyclin-dependent kinase inhibitor. Mutations in the FBXO7 (PARK15) gene have been implicated in a juvenile form of parkinsonism called parkinsonian pyramidal syndrome (PPS), characterized by Parkinsonian symptoms and pyramidal tract signs. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 341940693 333 LVVLPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLY 377
Cdd:cd22087    1 LLALPPEIKLRILSLLDVRSLLSLSQVCRDLNSATNDQLLWRFLL 45

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 341940693   1 MKLRVRLQK--RTQPLEVPESEpTLGQLRAHLSQvllpTLGFSSDtRFAITLNNKdALTGDEETLASYGIVSGDLICLV 77
Cdd:cd01796    1 MKLTVTTEDddRLFSLEVSPDM-TLEDLKALCEA----ETGIPAA-EQVLLHNGQ-PLTDDKKTLEALGLKDGDLLLLR 72

F-box domain found in F-box only protein 7 (FBXO7) and similar proteins; FBXO7, also called FBX7, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It recognizes BIRC2 and DLGAP5. FBXO7 plays a role downstream of PINK1 in the clearance of damaged mitochondria via selective autophagy (mitophagy) by targeting PRKN to dysfunctional depolarized mitochondria. It promotes MFN1 ubiquitination. FBXO7 acts as a cell cycle regulator by enhancing cyclin D/cyclin-dependent kinase 6 (Cdk6) complex formation and stabilizing levels of p27, a cyclin-dependent kinase inhibitor. Mutations in the FBXO7 (PARK15) gene have been implicated in a juvenile form of parkinsonism called parkinsonian pyramidal syndrome (PPS), characterized by Parkinsonian symptoms and pyramidal tract signs. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 341940693 333 LVVLPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLY 377
Cdd:cd22087    1 LLALPPEIKLRILSLLDVRSLLSLSQVCRDLNSATNDQLLWRFLL 45

F-box-like; This is an F-box-like family.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341940693  336 LPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLY 377
Cdd:pfam12937   4 LPDEILLQIFSYLDPKDLLRLALVCRRWRELASDDSLWRRLC 45

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 341940693  372 LWRCLYLRDF-----RDGTVRGPDTDWKELYRKKHIQRKE-----AQRMRHAM 414
Cdd:pfam06881  41 LWKRFIKRDFpnwaeEKDYEPKNPKSWRKLYEKLKEEREEklkaaAERLRQAY 93

F-box domain found in F-box only protein 7 (FBXO7) and similar proteins; FBXO7, also called FBX7, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It recognizes BIRC2 and DLGAP5. FBXO7 plays a role downstream of PINK1 in the clearance of damaged mitochondria via selective autophagy (mitophagy) by targeting PRKN to dysfunctional depolarized mitochondria. It promotes MFN1 ubiquitination. FBXO7 acts as a cell cycle regulator by enhancing cyclin D/cyclin-dependent kinase 6 (Cdk6) complex formation and stabilizing levels of p27, a cyclin-dependent kinase inhibitor. Mutations in the FBXO7 (PARK15) gene have been implicated in a juvenile form of parkinsonism called parkinsonian pyramidal syndrome (PPS), characterized by Parkinsonian symptoms and pyramidal tract signs. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 341940693 333 LVVLPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLY 377
Cdd:cd22087    1 LLALPPEIKLRILSLLDVRSLLSLSQVCRDLNSATNDQLLWRFLL 45

F-box-like; This is an F-box-like family.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341940693  336 LPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLY 377
Cdd:pfam12937   4 LPDEILLQIFSYLDPKDLLRLALVCRRWRELASDDSLWRRLC 45

F-box domain found in F-box only protein 9 (FBXO9) and similar proteins; FBXO9, also called FBX9, cross-immune reaction antigen 1, renal carcinoma antigen NY-REN-57, or VCIA1, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of TTI1 and TELO2 in a CK2-dependent manner, thereby directly regulating mTOR signaling. FBXO9 acts as an E3 ubiquitin ligase that regulates the stability and activity of peroxisome proliferator-activated receptor gamma (PPARgamma) through ubiquitination. It is also required for adipocyte differentiation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 341940693 335 VLPLELKLRIFRL----LDVHSVLALSAVCHDLLIASNDPLLWRCLYLR 379
Cdd:cd22089    5 ALPSEILLYILRWvvsdLDLRSLEQLSLVCRKFYLLARDPSIWRLACER 53

F-box domain found in F-box/LRR-repeat protein 4 (FBXL4) and similar proteins; FBXL4, also called F-box and leucine-rich repeat protein 4, or F-box protein FBL4/FBL5, is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It serves as a clock output molecule that regulates sleep through promotion of rhythmic degradation of the GABA(A) receptor. Biallelic pathogenic variants in FBXL4 are associated with an encephalopathic mtDNA maintenance defect syndrome that is a multi-system disease characterized by lactic acidemia, developmental delay, and hypotonia. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 341940693 335 VLPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLYLR 379
Cdd:cd22117    3 LLPYELIQLILSYLDLPSLCRLSQTCKLFRKHCYDPLLWKELNLQ 47

F-box domain superfamily; This short domain is commonly found at the N-terminus of various proteins, and typically co-occurs with one or more other conserved domains or motifs, such as leucine rich repeats, WD40 repeats, kelch, tub, spry, and others. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. One of the best researched roles of F-box proteins is their participation in SCF (Skp1-Cul1-F-box protein), a multi-protein complex that functions as a ubiquitin E3 ligase, where the role of the F-box protein is to recruit target substrates. Gene families containing the F-box are found greatly expanded in narrow taxonomic lineages, such as flowering plants and nematodes. In this hierarchical classification, many of the subfamilies are named according to their domain architectures.

                         10        20
                 ....*....|....*....|....*.
gi 341940693 336 LPLELKLRIFRLLDVHSVLALSAVCH 361
Cdd:cd09917    3 LPDEILLKILSYLDPRDLLRLSLVCK 28

F-box domain found in F-box only protein 21 (FBXO21) and similar proteins; FBXO21, also called FBX21, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It facilitates Lys29-linkage and activation of ASK1 (apoptosis signal-regulating kinase 1) and promotes type I interferon production upon viral infection. It also polyubiquitylates EP300-interacting inhibitor of differentiation 1 (EID1) and is required for the efficient degradation of EID1 in both cycling and quiescent cells. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 341940693 333 LVVLPLELKLRIF--RLLDVHSVLALSAVCHDLLIASNDPLLWRCLYL 378
Cdd:cd22096    1 LLELPDELLEYILcsDNLDHHDIIRLSCTCRRLREVCQSGKVWREKFF 48

F-box domain found in F-box/WD repeat-containing protein 5 (FBXW5) and similar proteins; FBXW5, also called F-box and WD-40 domain-containing protein 5, is the substrate-recognition component of both SCF (SKP1-CUL1-F-box protein) and DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 341940693 336 LPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLY 377
Cdd:cd22132    4 LPDSLLLHIFSYLSPKDLLAAGQVCKQWYRVSRDEFLWKELF 45

F-box domain found in F-box only protein 4 (FBXO4) and similar proteins; FBXO4, also called FBX4, is a specific substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that catalyzes the ubiquitination and subsequent degradation of cyclin D1 and Trx1. It recognizes TERF1 and promotes its ubiquitination together with UBE2D1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 341940693 336 LPLELKLRIFRLLDVHSVLALSAVCHDLLIASNDPLLWRCLYLRD 380
Cdd:cd22085    6 LPIDLQLYILSFLSPHDLCQLGLTSHYWHTLVRDPLLWRYFLLRD 50

ubiquitin-like (Ubl) domain found in ubiquitin thioesterase OTU1 and similar proteins; OTU1 (EC 3.4.19.12), also termed YOD1, or DUBA-8, or HIV-1-induced protease 7 (HIN-7), or OTU domain-containing protein 2 (OTUD2), is a p97-associated deubiquitinylase that functions as a key player in endoplasmic reticulum-associated degradation (ERAD). Its deubiquitinylase activity is also required for negatively regulating cholera toxin A1 (CTA1) retro-translocation. OTU1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a C2H2-type zinc finger, and an OTU domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940693   1 MKLRVRLQKRTQPLEVPESEPTLGQLRAHL---------SQVLLptLGFSsdtrfAITLNnkdaLTGDEETLASYGIVSG 71
Cdd:cd17059    1 MRLRVRSKGGQHVLSLLTDTSTVGELQDRIaaltgippsSQKIL--YGFP-----PKPLD----LSDEEASLESLGIQSG 69

                 ...
gi 341940693  72 DLI 74
Cdd:cd17059   70 DTL 72