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Conserved domains on  [gi|31563518|ref|NP_852610|]
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microtubule-associated proteins 1A/1B light chain 3A isoform b [Homo sapiens]

Protein Classification

ubiquitin family protein( domain architecture ID 1000087)

ubiquitin family protein belongs to an diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 18-124 3.42e-75

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.


The actual alignment was detected with superfamily member cd17234:

Pssm-ID: 475130  Cd Length: 117  Bit Score: 218.38  E-value: 3.42e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  18 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 97
Cdd:cd17234  11 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 90

                        90       100
                ....*....|....*....|....*..
gi 31563518  98 PIADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:cd17234  91 PIADIYEQEKDEDGFLYMVYASQETFG 117
 
Name Accession Description Interval E-value
Ubl_ATG8_MAP1LC3A cd17234
ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3A (MAP1LC3A); ...
 18-124 3.42e-75

ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3A (MAP1LC3A); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3A is belong to MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like fold (Ubl) that belongs to the autophagy-related 8 (ATG8) 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 cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAPLC3 is known as a marker of autophagy-induction. MAP1LC3A staining patterns are used for different cancer diagnostic.


Pssm-ID: 340754  Cd Length: 117  Bit Score: 218.38  E-value: 3.42e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  18 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 97
Cdd:cd17234  11 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 90

                        90       100
                ....*....|....*....|....*..
gi 31563518  98 PIADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:cd17234  91 PIADIYEQEKDEDGFLYMVYASQETFG 117
ATG8 pfam02991
Autophagy protein Atg8 ubiquitin like; Light chain 3 is proposed to function primarily as a ...
 20-124 1.00e-51

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.


Pssm-ID: 281049  Cd Length: 104  Bit Score: 158.67  E-value: 1.00e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518    20 RCKEVQQIRDQHPSKIPVIIERYKGEKqLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQhSMVSVSTPI 99
Cdd:pfam02991   2 RQKESEKIREKYPDRIPVIIEKASGSD-LPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNN-TLPPTSATM 79

                          90       100
                  ....*....|....*....|....*
gi 31563518   100 ADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:pfam02991  80 SALYEEEKDEDGFLYMVYSGENTFG 104
 
Name Accession Description Interval E-value
Ubl_ATG8_MAP1LC3A cd17234
ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3A (MAP1LC3A); ...
 18-124 3.42e-75

ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3A (MAP1LC3A); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3A is belong to MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like fold (Ubl) that belongs to the autophagy-related 8 (ATG8) 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 cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAPLC3 is known as a marker of autophagy-induction. MAP1LC3A staining patterns are used for different cancer diagnostic.


Pssm-ID: 340754  Cd Length: 117  Bit Score: 218.38  E-value: 3.42e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  18 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 97
Cdd:cd17234  11 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 90

                        90       100
                ....*....|....*....|....*..
gi 31563518  98 PIADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:cd17234  91 PIADIYEQEKDEDGFLYMVYASQETFG 117
Ubl_ATG8_MAP1LC3 cd16129
ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3 (MAP1LC3); ...
 19-123 6.20e-75

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.


Pssm-ID: 340546  Cd Length: 105  Bit Score: 217.21  E-value: 6.20e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  19 DRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTP 98
Cdd:cd16129   1 QRKKDVEEIREKHPNKIPVIIERYKGEKQLPLLDKTKFLVPDHVTMSELVKIIRRRLQLNPTQAFFLLVNQRSMVSVSTP 80

                        90       100
                ....*....|....*....|....*
gi 31563518  99 IADIYEQEKDEDGFLYMVYASQETF 123
Cdd:cd16129  81 MSEVYRREKDEDGFLYMVYASQETF 105
Ubl_ATG8_MAP1LC3B cd17235
ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3B (MAP1LC3B); ...
 20-123 3.59e-60

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.


Pssm-ID: 340755  Cd Length: 115  Bit Score: 180.70  E-value: 3.59e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  20 RCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPI 99
Cdd:cd17235  12 RVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPI 91

                        90       100
                ....*....|....*....|....
gi 31563518 100 ADIYEQEKDEDGFLYMVYASQETF 123
Cdd:cd17235  92 SEVYESEKDEDGFLYMVYASQETF 115
ATG8 pfam02991
Autophagy protein Atg8 ubiquitin like; Light chain 3 is proposed to function primarily as a ...
 20-124 1.00e-51

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.


Pssm-ID: 281049  Cd Length: 104  Bit Score: 158.67  E-value: 1.00e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518    20 RCKEVQQIRDQHPSKIPVIIERYKGEKqLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQhSMVSVSTPI 99
Cdd:pfam02991   2 RQKESEKIREKYPDRIPVIIEKASGSD-LPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNN-TLPPTSATM 79

                          90       100
                  ....*....|....*....|....*
gi 31563518   100 ADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:pfam02991  80 SALYEEEKDEDGFLYMVYSGENTFG 104
Ubl_ATG8_MAP1LC3C cd17236
ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3C (MAPLC3C); ...
 18-123 7.86e-51

ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3C (MAPLC3C); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3C belongs to the MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like (Ubl) fold that belongs to the autophagy-related 8 (ATG8) 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 cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, a E2-like enzyme. The Ubl conversion of MAP1LC3 is known as a marker of autophagy-induction. ATG8 proteins are ubiquitously expressed, although some subfamily members are expressed at increased levels in certain tissues, e.g. MAP1LC3C is transcribed at lower levels than other members of MAP1LC3 subfamily and expressed predominantly in the lung.


Pssm-ID: 340756  Cd Length: 113  Bit Score: 156.83  E-value: 7.86e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  18 ADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVST 97
Cdd:cd17236   8 ASRKEEVAGIRAKFPNKIPVIVERYYKEKNLPILDKTKFLVPQELTMSQFVTIIRNRMSLTATQAFYLLVNNKSLASMST 87

                        90       100
                ....*....|....*....|....*.
gi 31563518  98 PIADIYEQEKDEDGFLYMVYASQETF 123
Cdd:cd17236  88 TMAEVYRDEKDEDGFLYMTYASQEMF 113
Ubl_Autophagy_like cd01611
ubiquitin-like (Ubl) domain found in autophagy-related ubiquitin-like protein; Autophagy is an ...
 34-119 2.99e-36

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).


Pssm-ID: 340453  Cd Length: 84  Bit Score: 119.07  E-value: 2.99e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  34 KIPVIIERYKGEKqLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSvSTPIADIYEQEKDEDGFL 113
Cdd:cd01611   1 KIPVILEKAGKTK-IPILDKKKYLVPRDLTVGQLIDFIRKRLKLVAEEALFIFVNQFAPPT-SAEMGTLYEEHGDEDGFL 78


                ....*.
gi 31563518 114 YMVYAS 119
Cdd:cd01611  79 YLHYSK 84
Ubl_ATG8_like cd16108
ubiquitin-like (Ubl) domain found in autophagy-related 8 (ATG8) and similar proteins; The ATG8 ...
 34-119 9.02e-34

ubiquitin-like (Ubl) domain found in autophagy-related 8 (ATG8) and similar proteins; The ATG8 family of proteins constitute a single member in Saccharomyces cerevisiae, Atg8p, and multiple homologs in higher eukaryotes, they are multifunctional ubiquitin-like (Ubl) key regulators of autophagy. The ATG8 system is a Ubl conjugation system that is essential for autophagosome formation. In the ATG8 system, a cysteine protease (ATG4) cleaves a C-terminal arginine from ATG8, and then the exposed C-terminal glycine is conjugated to phosphatidylethanolamine (PE) by ATG7, an E1-like enzyme, and ATG3, an E2-like enzyme. 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).


Pssm-ID: 340525  Cd Length: 85  Bit Score: 112.67  E-value: 9.02e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  34 KIPVIIERYKGeKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSvSTPIADIYEQEKDEDGFL 113
Cdd:cd16108   2 RIPVIVEKAPK-SDLPDIDKKKFLVPSDLTVGQFMYIIRKRIKLSPEKAIFLFVNNTLPPT-SALMSEVYEEYKDEDGFL 79


                ....*.
gi 31563518 114 YMVYAS 119
Cdd:cd16108  80 YVKYSG 85
Ubl_ATG8_GABARAPL2 cd17163
ubiquitin-like (Ubl) domain found in GABA type A receptor associated protein like 2 (GABARAPL2, ...
 20-124 2.51e-29

ubiquitin-like (Ubl) domain found in GABA type A receptor associated protein like 2 (GABARAPL2, also known as GATE16); Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. GABARAPL2 (GABA type A receptor associated protein like 2), also known as GATE-16 (golgi-associated adenosine triphosphatase enhancer of 16 kDa), has a ubiquitin-like (Ubl) domain and is a sub-family of the autophagy-related 8 (ATG8) protein family. GABARAPL2 participates to the autophagosome maturation, and seems to be involved in constitutive transport under normal conditions and in autophagic processes during stress. GABARAPL2 is characterized as a membrane transport modulator that controls intra-Golgi transport by interacting with NSF and Golgi v-SNARE GOS-28.


Pssm-ID: 340683  Cd Length: 112  Bit Score: 102.11  E-value: 2.51e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  20 RCKEVQQIRDQHPSKIPVIIERYKGEkQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQhSMVSVSTPI 99
Cdd:cd17163  10 RCAESAKIRAKYPDRIPVIVEKVPKS-QIPDIDKRKFLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVGK-VLPQSSATM 87

                        90       100
                ....*....|....*....|....*
gi 31563518 100 ADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:cd17163  88 GQLYEEHKDEDGFLYVAYSGENTFG 112
Ubl_ATG8 cd16128
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae Atg8p and related proteins; ...
 20-120 4.84e-24

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.


Pssm-ID: 340545  Cd Length: 103  Bit Score: 88.67  E-value: 4.84e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  20 RCKEVQQIRDQHPSKIPVIIEryKGEK-QLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQhSMVSVSTP 98
Cdd:cd16128   4 RKAEAERIRDKYPDRIPVICE--KAEKsDIPDIDKKKYLVPADLTVGQFVYVIRKRIKLSPEKAIFIFVNN-VLPPTAAL 80

                        90       100
                ....*....|....*....|..
gi 31563518  99 IADIYEQEKDEDGFLYMVYASQ 120
Cdd:cd16128  81 MSAIYEEHKDEDGFLYVTYSGE 102
Ubl_ATG8_GABARAP_like cd16127
ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein ...
 20-118 6.07e-19

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.


Pssm-ID: 340544  Cd Length: 107  Bit Score: 75.60  E-value: 6.07e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  20 RCKEVQQIRDQHPSKIPVIIERyKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNqHSMVSVSTPI 99
Cdd:cd16127  10 RRSEGEKIRKKYPDRVPVIVEK-APKARVADLDKKKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVN-NVIPPTSATM 87

                        90
                ....*....|....*....
gi 31563518 100 ADIYEQEKDEDGFLYMVYA 118
Cdd:cd16127  88 GQLYQEHHEEDFFLYIAYS 106
Ubl_ATG8_GABARAPL1_like cd17233
ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein-like ...
 20-118 4.08e-18

ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein-like 1 (GABARAPL1) and similar proteins; GABARAPL1, also termed GEC1, or GABA(A) receptor-associated protein-like, belongs to the small family of GABARAP proteins which includes GABARAP, GABARAPL1, 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. It 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. This family also includes GABARAPL3, a paralog of GABARAPL1.


Pssm-ID: 340753  Cd Length: 107  Bit Score: 73.56  E-value: 4.08e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  20 RCKEVQQIRDQHPSKIPVIIERYKgEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNqHSMVSVSTPI 99
Cdd:cd17233  10 RKKEGEKIRKKYPDRVPVIVEKAP-KARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVN-NTIPPTSATM 87

                        90
                ....*....|....*....
gi 31563518 100 ADIYEQEKDEDGFLYMVYA 118
Cdd:cd17233  88 GQLYEDNHEEDYFLYVAYS 106
Ubl_ATG8_GABARAP cd17232
ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein ...
 20-124 6.76e-17

ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein (GABARAP); GABARAP (also termed GABA(A) receptor-associated protein, ATG8A, or MM46) has been implicated in intracellular protein trafficking. It is a cytosolic protein that is 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.


Pssm-ID: 340752  Cd Length: 115  Bit Score: 70.79  E-value: 6.76e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31563518  20 RCKEVQQIRDQHPSKIPVIIERYKgEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNqHSMVSVSTPI 99
Cdd:cd17232  13 RRSEGEKIRKKYPDRVPVIVEKAP-KARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVN-NVIPPTSATM 90

                        90       100
                ....*....|....*....|....*
gi 31563518 100 ADIYEQEKDEDGFLYMVYASQETFG 124
Cdd:cd17232  91 GQLYQEHHEEDFFLYIAYSDESVYG 115
APG12 pfam04110
Ubiquitin-like autophagy protein Apg12; In yeast, 15 Apg proteins coordinate the formation of ...
 49-124 6.10e-03

Ubiquitin-like autophagy protein Apg12; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukaryotes. It was first discovered in yeast during systematic analyses of the apg mutants defective in autophagy. Covalent attachment of Apg12-Apg5 is essential for autophagy.


Pssm-ID: 397985  Cd Length: 87  Bit Score: 33.54  E-value: 6.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 31563518    49 PVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKdEDGFLYMVYASQETFG 124
Cdd:pfam04110  13 PILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFG-TDGKLVLNYCISVAWG 87
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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