Autophagy protein Atg8 ubiquitin like; Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  59 KRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMG 138
Cdd:pfam02991   1 KRQKESEKIREKYPDRIPVIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNNTLPPTSATMS 80

                          90       100
                  ....*....|....*....|....
gi 1148885655 139 QLYQEHHEEDFFLYIAYSDESVYG 162
Cdd:pfam02991  81 ALYEEEKDEDGFLYMVYSGENTFG 104

ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein (GABARAP) and similar proteins; sub-family of the autophagy-related 8 (ATG8) protein family; GABARAP (also termed GABA(A) receptor-associated protein, ATG8A, or MM46) has been implicated in intracellular protein trafficking. It is a cytosolic protein, localized to transport vesicles, the Golgi network and the endoplasmic reticulum. It interacts with the intracellular domain of the gamma2 subunit of GABA(A) receptors, and thus, functions as a trafficking modulator implicated in the intracellular trafficking of GABA(A) receptor. GABARAP also acts as a Ubl modifier belonging to the ATG8 (autophagy-related 8) protein family which is essential for autophagosome biogenesis and maturation. GABARAP recruits phosphatidylinositol 4-kinase II alpha (PI4KIIalpha) as a specific downstream effector, and regulates phosphatidylinositol 4-phosphate (PI4P)-dependent autophagosome lysosome fusion. This sub-family also includes GABARAPL1 (also termed GABA(A) receptor-associated protein-like, or GEC1), GABARAPL2/GATE-16, and GABARAPL3. GABARAPL1 has been involved in the intracellular transport of receptors via interactions with tubulin and GABA(A) or kappa opioid receptors. GABARAPL1 is also a Ubl modifier that functions as a mediator involved in androgen-regulated autophagy process. It is transcriptionally modulated by androgen receptor (AR) and has a repressive role in autophagy. In addition, GABARAPL1 is required for increased membrane expression of epidermal growth factor receptor (EGFR) during hypoxia, suggesting a possible role in the trafficking of these membrane proteins. GABARAPL1 may also play a key role in several important biological processes such as cancer or neurodegenerative diseases. Low expression of GABARAPL1 is associated with poor prognosis of patients with hepatocellular carcinoma.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  51 YKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVI 130
Cdd:cd16127     1 YKEDHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARVADLDKKKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNVI 80

                          90       100
                  ....*....|....*....|....*..
gi 1148885655 131 PPTSATMGQLYQEHHEEDFFLYIAYSD 157
Cdd:cd16127    81 PPTSATMGQLYQEHHEEDFFLYIAYSD 107

Autophagy protein Atg8 ubiquitin like; Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  59 KRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMG 138
Cdd:pfam02991   1 KRQKESEKIREKYPDRIPVIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNNTLPPTSATMS 80

                          90       100
                  ....*....|....*....|....
gi 1148885655 139 QLYQEHHEEDFFLYIAYSDESVYG 162
Cdd:pfam02991  81 ALYEEEKDEDGFLYMVYSGENTFG 104

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae Atg8p and related proteins; sub-family of the autophagy-related 8 (ATG8) family; The ATG8 family of proteins constitutes a single member in Saccharomyces cerevisiae, Atg8p, and multiple homologs in higher eukaryotes. These proteins are multifunctional ubiquitin-like (Ubl) key regulators of autophagy. ATG8 is characterized by a C-terminal ubiquitin-like (Ubl) domain with a short N-terminal extension. The covalent attachment of ATG8 to phosphatidylethanolamine (PtdEth) at the autophagosomal membrane places it at a crucial juncture during autophagosome formation. ATG Ubl proteins such as Saccharomyces cerevisiae Atg8p undergo a unique Ubl conjugation, a process essential for autophagosome formation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  57 FEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSAT 136
Cdd:cd16128     1 FEKRKAEAERIRDKYPDRIPVICEKAEKSDIPDIDKKKYLVPADLTVGQFVYVIRKRIKLSPEKAIFIFVNNVLPPTAAL 80

                          90       100
                  ....*....|....*....|...
gi 1148885655 137 MGQLYQEHHEEDFFLYIAYSDES 159
Cdd:cd16128    81 MSAIYEEHKDEDGFLYVTYSGEN 103

ubiquitin-like (Ubl) domain found in autophagy-related ubiquitin-like protein; Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. The autophagy-related ubiquitin-like proteins, such as Saccharomyces cerevisiae Atg8p, undergo a unique ubiquitin-like (Ubl) conjugation, a process essential for autophagosome formation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The ubiquitination process comprises a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. ATG8 family proteins undergo multistep modifications by the E1-like (ubiquitin activating) enzyme ATG7, and the E2-like (ubiquitin conjugating) enzyme ATG3. The mammalian ATG8 family is classified into three subfamilies: i) MAP1LC3 (microtubule associated protein 1 light chain 3) which includes MAP1LC3A, MAP1LC3B, MAP1LC3B2, and MAP1LC3C, ii) GABARAP (GABA type A receptor associated protein) which includes GABARAP, GABARAPL1, and GABARAPL3, and iii) GABARAPL2 (GABA type A receptor associated protein like 2), also known as GATE-16 (golgi-associated adenosine triphosphatase enhancer of 16 kDa).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  74 RVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYI 153
Cdd:cd01611     1 KIPVILEKAGKTKIPILDKKKYLVPRDLTVGQLIDFIRKRLKLVAEEALFIFVNQFAPPTSAEMGTLYEEHGDEDGFLYL 80

                  ....
gi 1148885655 154 AYSD 157
Cdd:cd01611    81 HYSK 84

ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3 (MAP1LC3); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3 (also known as LC3) has a ubiquitin-like (Ubl) fold and belongs to the ATG8 autophagy protein family. A Ubl conjugation of MAP1LC3 by the phospholipid phosphatidylethanolamine (PE) is an essential process for the formation of autophagosomes. MAP1LC3 is cleaved by the cysteine protease ATG4 and is then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAP1LC3 is known as a marker of autophagy-induction. This sub-family includes MAP1LC3A, MAP1LC3B, and MAP1LC3C, each encoded by a different MAP1LC3 gene.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  60 RRSEGEKIRKKYPDRVPVIVEKAPKAR-IGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNN-VIPPTSATM 137
Cdd:cd16129     2 RKKDVEEIREKHPNKIPVIIERYKGEKqLPLLDKTKFLVPDHVTMSELVKIIRRRLQLNPTQAFFLLVNQrSMVSVSTPM 81

                          90       100
                  ....*....|....*....|....
gi 1148885655 138 GQLYQEHHEEDFFLYIAYSDESVY 161
Cdd:cd16129    82 SEVYRREKDEDGFLYMVYASQETF 105

ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3B (MAP1LC3B); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAPLC3B belongs to the MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like (Ubl) fold and belongs to the autophagy-related 8 (ATG8) protein family. A Ubl conjugation of MAPLC3 by the phospholipid phosphatidylethanolamine (PE) is an essential process for the formation of autophagosomes. MAP1LC3 is cleaved by cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAP1LC3 is known as a marker of autophagy-induction. All MAP1LC3 proteins are dispensable for basal autophagy; however, it has been shown that MAP1LC3B is responsible for selective degradation of p62 through autophagy.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148885655  51 YKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAP-KARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVN-N 128
Cdd:cd17235     3 FKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKgEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNgH 82

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1148885655 129 VIPPTSATMGQLYQEHHEEDFFLYIAYSDESVY 161
Cdd:cd17235    83 SMVSVSTPISEVYESEKDEDGFLYMVYASQETF 115

Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1148885655  84 KARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLrAEDALFFFVNNVIPPTSATMGQlyqehHEEDFFLYIAYS 156
Cdd:cd00196     2 KVETPSLKKIVVAVPPSTTLRQVLEKVAKRIGL-PPDVIRLLFNGQVLDDLMTAKQ-----VGLEPGEELHFV 68

ubiquitin-like (Ubl) domain found in autophagy-related protein 12 (ATG12); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. The autophagy-related ubiquitin-like (Ubl) proteins such as ATG12 protein have a conserved Ubl fold structure and undergo a unique Ubl conjugation, a process essential for autophagosome formation. ATG12 is conjugated to ATG5 by multistep modifications of the E1-like (ubiquitin activating) enzyme ATG7, and the E2-like (ubiquitin conjugating) enzyme ATG10. The ATG12-ATG5 conjugate facilitates the lipidation of ATG8 and directs its correct subcellular localization. ATG12 is localized at the developing autophagosome.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1148885655  87 IGD---LDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPT-SATMGQLYQEHHEEDfFLYIAYS 156
Cdd:cd01612     9 VGDapiLKQKKFKVSASQKFASVIDFLRKQLKLKPSESLFLYINQSFAPSpDEEVGDLYDCFGSNG-KLVLNYC 81