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Conserved domains on  [gi|195589736|ref|XP_002084605|]
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autophagy protein 12-like [Drosophila simulans]

Protein Classification

APG12_C domain-containing protein( domain architecture ID 10513777)

APG12_C domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
APG12 pfam04110
Ubiquitin-like autophagy protein Apg12; In yeast, 15 Apg proteins coordinate the formation of ...
 25-111 6.29e-50

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: 152.95  E-value: 6.29e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736   25 KICILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPDQIIKNLYECHGTNGKLVLYY 104
Cdd:pfam04110   1 KITIRLRAIGDAPILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFGTDGKLVLNY 80


                  ....*..
gi 195589736  105 CKNQAWG 111
Cdd:pfam04110  81 CISVAWG 87
 
Name Accession Description Interval E-value
APG12 pfam04110
Ubiquitin-like autophagy protein Apg12; In yeast, 15 Apg proteins coordinate the formation of ...
 25-111 6.29e-50

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: 152.95  E-value: 6.29e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736   25 KICILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPDQIIKNLYECHGTNGKLVLYY 104
Cdd:pfam04110   1 KITIRLRAIGDAPILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFGTDGKLVLNY 80


                  ....*..
gi 195589736  105 CKNQAWG 111
Cdd:pfam04110  81 CISVAWG 87
Ubl_ATG12 cd01612
ubiquitin-like (Ubl) domain found in autophagy-related protein 12 (ATG12); Autophagy is an ...
 25-110 4.95e-47

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.


Pssm-ID: 340454  Cd Length: 86  Bit Score: 145.74  E-value: 4.95e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736  25 KICILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPDQIIKNLYECHGTNGKLVLYY 104
Cdd:cd01612    1 KVVVLFKAVGDAPILKQKKFKVSASQKFASVIDFLRKQLKLKPSESLFLYINQSFAPSPDEEVGDLYDCFGSNGKLVLNY 80


                 ....*.
gi 195589736 105 CKNQAW 110
Cdd:cd01612   81 CKTPAW 86
 
Name Accession Description Interval E-value
APG12 pfam04110
Ubiquitin-like autophagy protein Apg12; In yeast, 15 Apg proteins coordinate the formation of ...
 25-111 6.29e-50

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: 152.95  E-value: 6.29e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736   25 KICILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPDQIIKNLYECHGTNGKLVLYY 104
Cdd:pfam04110   1 KITIRLRAIGDAPILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFGTDGKLVLNY 80


                  ....*..
gi 195589736  105 CKNQAWG 111
Cdd:pfam04110  81 CISVAWG 87
Ubl_ATG12 cd01612
ubiquitin-like (Ubl) domain found in autophagy-related protein 12 (ATG12); Autophagy is an ...
 25-110 4.95e-47

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.


Pssm-ID: 340454  Cd Length: 86  Bit Score: 145.74  E-value: 4.95e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736  25 KICILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPDQIIKNLYECHGTNGKLVLYY 104
Cdd:cd01612    1 KVVVLFKAVGDAPILKQKKFKVSASQKFASVIDFLRKQLKLKPSESLFLYINQSFAPSPDEEVGDLYDCFGSNGKLVLNY 80


                 ....*.
gi 195589736 105 CKNQAW 110
Cdd:cd01612   81 CKTPAW 86
Ubl_Autophagy_like cd01611
ubiquitin-like (Ubl) domain found in autophagy-related ubiquitin-like protein; Autophagy is an ...
 25-106 4.84e-21

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: 79.78  E-value: 4.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736  25 KICILLNATG--NVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQtFAPAPDQIIKNLYECHGT-NGKLV 101
Cdd:cd01611    1 KIPVILEKAGktKIPILDKKKYLVPRDLTVGQLIDFIRKRLKLVAEEALFIFVNQ-FAPPTSAEMGTLYEEHGDeDGFLY 79


                 ....*
gi 195589736 102 LYYCK 106
Cdd:cd01611   80 LHYSK 84
Ubl_ATG8_like cd16108
ubiquitin-like (Ubl) domain found in autophagy-related 8 (ATG8) and similar proteins; The ATG8 ...
 35-94 4.69e-05

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: 38.71  E-value: 4.69e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736  35 NVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTfAPAPDQIIKNLYECH 94
Cdd:cd16108   14 DLPDIDKKKFLVPSDLTVGQFMYIIRKRIKLSPEKAIFLFVNNT-LPPTSALMSEVYEEY 72
ATG8 pfam02991
Autophagy protein Atg8 ubiquitin like; Light chain 3 is proposed to function primarily as a ...
 36-94 4.30e-04

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: 36.56  E-value: 4.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 195589736   36 VPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFaPAPDQIIKNLYECH 94
Cdd:pfam02991  29 LPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNNTL-PPTSATMSALYEEE 86
RAWUL_PCGF_like cd16102
RRING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in PCGF1-6, RING1 and -2, ...
 27-104 6.92e-04

RRING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in PCGF1-6, RING1 and -2, DRIP and similar proteins; structurally similar to a beta-grasp ubiquitin-like fold; The family includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies that can remodel chromatin such that epigenetic silencing of genes takes place, and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development in fruit flies. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which are involved in the maintenance of gene repression and target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins, have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger, and a RAWUL domain that might be responsible for interaction with Cbx members of the Polycomb repression complexes.


Pssm-ID: 340519  Cd Length: 87  Bit Score: 35.72  E-value: 6.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195589736  27 CILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPaPDQIIKNLYEC--HGTNGKLVLYY 104
Cdd:cd16102    8 PSESNLGGKLPQLEKPYLRCSARATVGHLKKFLRRKLKLDSEQDLDILCRGELLG-KEHTLKFIWRTrwRKQDGPLVLQY 86
Ubl_ATG8 cd16128
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae Atg8p and related proteins; ...
 34-94 9.15e-04

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: 35.90  E-value: 9.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 195589736  34 GNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPdQIIKNLYECH 94
Cdd:cd16128   29 SDIPDIDKKKYLVPADLTVGQFVYVIRKRIKLSPEKAIFIFVNNVLPPTA-ALMSAIYEEH 88
NR_LBD_SHP cd07349
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 28-84 1.26e-03

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.


Pssm-ID: 132763  Cd Length: 222  Bit Score: 36.34  E-value: 1.26e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 195589736  28 ILLNATGNVPIIKKRTWTVDPNKTVSWIQKFIHKFLKLDASEQIFLYVNQTFAPAPD 84
Cdd:cd07349   90 ILLEGQSSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPD 146
RAWUL_PCGF6 cd17085
RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING ...
 51-105 7.37e-03

RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 6 (PCGF6) and similar proteins; PCGF6, also termed Mel18 and Bmi1-like RING finger (MBLR), or RING finger protein 134 (RNF134), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5 and PCGF6/MBLR), and serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like L3MBTL2 complex, which is composed of some canonical components, such as RNF2, CBX3, CXB4, CXB6, CXB7 and CXB8, as well as some noncanonical components, such as L3MBTL2, E2F6, WDR5, HDAC1 and RYBP, and plays critical roles in epigenetic transcriptional silencing in higher eukaryotes. Like other PCGF homologs, PCGF6 possesses the transcriptional repression activity, and also associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF6 can regulate the enzymatic activity of JARID1d/KDM5D, a trimethyl H3K4 demethylase, through the direct interaction with it. Furthermore, PCGF6 is expressed predominantly in meiotic and post-meiotic male germ cells and may play important roles in mammalian male germ cell development. It also regulates mesodermal lineage differentiation in mammalian embryonic stem cells (ESCs) and functions in induced pluripotent stem (iPS) reprogramming. The activity of PCGF6 is found to be regulated by cell cycle dependent phosphorylation. PCGF6 contains a C3HC4-type RING-HC finger, and a RAWUL domain.


Pssm-ID: 340605  Cd Length: 89  Bit Score: 33.02  E-value: 7.37e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 195589736  51 TVSWIQKFIHKFLKLDASEQIFLYVNQTFAPaPDQIIKNLYE--CHG-TNGKLVLYYC 105
Cdd:cd17085   33 TVGHVEKFLRKKLNLDSTCEVDILCGEHILE-NYQTLREIRDqfGDGaQDGLLVLHYG 89
 
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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