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Conserved domains on  [gi|1958752425|ref|XP_038958954|]
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reticulophagy regulator 1 isoform X3 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arl6IP1_RETR3-like super family cl41772
ADP-ribosylation factor-like protein 6-interacting protein 1, Reticulophagy regulator 3, and ...
 9-115 5.48e-77

ADP-ribosylation factor-like protein 6-interacting protein 1, Reticulophagy regulator 3, and similar proteins; This family contains ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1) and the N-terminal reticulon-homology domain (RHD) of Reticulophagy regulators 1-3. Arl6IP1 is an endoplasmic reticulum (ER) protein that has an important role in cell conduction and material transport. Arl6IP1, a tetraspan membrane protein, is an anti-apoptotic protein specific to multicellular organisms, and is a potential player in shaping the ER tubules in mammalian cells. In Drosophila, knockdown of the Arl6IP1 gene leads to progressive motor deficit. An Arl6IP1 variant has also been associated with hereditary spastic paraplegia (HSP), motor and sensory polyneuropathy, and acromutilation. Reticulophagy regulator 1 (RETREG1/FAM134B) is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. RETREG2/FAM134A and RETREG3/FAM134C has been shown to interact with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. Arl6IP1 shows some sequence similarity to the RHD of reticulophagy regulators, which may function in inducing membrane curvature.


The actual alignment was detected with superfamily member cd22560:

Pssm-ID: 425403  Cd Length: 198  Bit Score: 235.03  E-value: 5.48e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425   9 SWEVINSKPDERPRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPL 88
Cdd:cd22560    92 SWEVIDSKPDERPRLSQCIAESWMNFSAFLQEMSHFKQQNPGKFCLLVCSVCTFFTILGSYIPGVVLSYLLLLCAFLCPL 171

                          90       100
                  ....*....|....*....|....*..
gi 1958752425  89 FKCNDIGQKIYSKVKSILLKLDFGIGE 115
Cdd:cd22560   172 FKCNEFGQKVYSKVKSVLQKLDFGIGE 198
rad2 super family cl36701
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 126-235 7.21e-03

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00600:

Pssm-ID: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 38.34  E-value: 7.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425  126 EADKEKSHKDDSEIDFSALCPKISLTVAAKELS---VSDTDVSEVSWTDNGTFNLSEGYTPQTDTSDDLDRPSEEvfSRD 202
Cdd:TIGR00600  648 ESEKEESESDGSFIEVDSVSSTLELQVPSKSQPtdeSEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEE--EKD 725

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958752425  203 LSDFPSLENGAGTNDEDELS---LGLPTELKTKKQQ 235
Cdd:TIGR00600  726 ADDFKNEWQDISLEELEALEanlLAEQNSLKAQKQQ 761
 
Name Accession Description Interval E-value
RETR1_RHD cd22560
N-terminal reticulon-homology domain of Reticulophagy regulator 1; Reticulophagy regulator 1 ...
 9-115 5.48e-77

N-terminal reticulon-homology domain of Reticulophagy regulator 1; Reticulophagy regulator 1 (RETR1 or RETREG1), also called reticulophagy receptor 1 or FAM134B (family with sequence similarity 134, member B), is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. Loss of function of FAM134B is associated with diseases and cancer, including hereditary sensory and autonomic neuropathy type IIB (HSAN IIB), colorectal adenocarcinoma, and oesophageal squamous cell carcinoma, and other progressive neuronal degenerative diseases. FAM134B is also implicated in the suppression of viral replication during Ebola, Dengue, Zika, and West Nile viral infections. RETREG1/FAM134B contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an ER protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature.


Pssm-ID: 411699  Cd Length: 198  Bit Score: 235.03  E-value: 5.48e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425   9 SWEVINSKPDERPRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPL 88
Cdd:cd22560    92 SWEVIDSKPDERPRLSQCIAESWMNFSAFLQEMSHFKQQNPGKFCLLVCSVCTFFTILGSYIPGVVLSYLLLLCAFLCPL 171

                          90       100
                  ....*....|....*....|....*..
gi 1958752425  89 FKCNDIGQKIYSKVKSILLKLDFGIGE 115
Cdd:cd22560   172 FKCNEFGQKVYSKVKSVLQKLDFGIGE 198
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 126-235 7.21e-03

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 38.34  E-value: 7.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425  126 EADKEKSHKDDSEIDFSALCPKISLTVAAKELS---VSDTDVSEVSWTDNGTFNLSEGYTPQTDTSDDLDRPSEEvfSRD 202
Cdd:TIGR00600  648 ESEKEESESDGSFIEVDSVSSTLELQVPSKSQPtdeSEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEE--EKD 725

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958752425  203 LSDFPSLENGAGTNDEDELS---LGLPTELKTKKQQ 235
Cdd:TIGR00600  726 ADDFKNEWQDISLEELEALEanlLAEQNSLKAQKQQ 761
 
Name Accession Description Interval E-value
RETR1_RHD cd22560
N-terminal reticulon-homology domain of Reticulophagy regulator 1; Reticulophagy regulator 1 ...
 9-115 5.48e-77

N-terminal reticulon-homology domain of Reticulophagy regulator 1; Reticulophagy regulator 1 (RETR1 or RETREG1), also called reticulophagy receptor 1 or FAM134B (family with sequence similarity 134, member B), is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. Loss of function of FAM134B is associated with diseases and cancer, including hereditary sensory and autonomic neuropathy type IIB (HSAN IIB), colorectal adenocarcinoma, and oesophageal squamous cell carcinoma, and other progressive neuronal degenerative diseases. FAM134B is also implicated in the suppression of viral replication during Ebola, Dengue, Zika, and West Nile viral infections. RETREG1/FAM134B contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an ER protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature.


Pssm-ID: 411699  Cd Length: 198  Bit Score: 235.03  E-value: 5.48e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425   9 SWEVINSKPDERPRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPL 88
Cdd:cd22560    92 SWEVIDSKPDERPRLSQCIAESWMNFSAFLQEMSHFKQQNPGKFCLLVCSVCTFFTILGSYIPGVVLSYLLLLCAFLCPL 171

                          90       100
                  ....*....|....*....|....*..
gi 1958752425  89 FKCNDIGQKIYSKVKSILLKLDFGIGE 115
Cdd:cd22560   172 FKCNEFGQKVYSKVKSVLQKLDFGIGE 198
RETR_RHD cd22558
N-terminal reticulon-homology domain of Reticulophagy regulators and similar proteins; This ...
 9-115 1.75e-51

N-terminal reticulon-homology domain of Reticulophagy regulators and similar proteins; This subfamily includes Reticulophagy regulators 1-3. Reticulophagy regulator 1 (RETREG1/FAM134B) is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. RETREG2/FAM134A and RETREG3/FAM134C has been shown to interact with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. Members of this subfamily contain an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an ER protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature.


Pssm-ID: 411697  Cd Length: 192  Bit Score: 169.41  E-value: 1.75e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425   9 SWEVINSKPDERPRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPL 88
Cdd:cd22558    86 SWTPIHPRLLSVPELCRHLAESWVSFTIFLQKLWQFRKQHPGKFCLLVCSFCTCLAVIGHYVPGVLLSYIILLSLLLWPL 165

                          90       100
                  ....*....|....*....|....*..
gi 1958752425  89 FKCNDIGQKIYSKVKSILLKLDFGIGE 115
Cdd:cd22558   166 VVYHRVPQKIYTKLEPVLMQLEYSMKI 192
Arl6IP1_RETR3-like cd21102
ADP-ribosylation factor-like protein 6-interacting protein 1, Reticulophagy regulator 3, and ...
 4-112 2.94e-47

ADP-ribosylation factor-like protein 6-interacting protein 1, Reticulophagy regulator 3, and similar proteins; This family contains ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1) and the N-terminal reticulon-homology domain (RHD) of Reticulophagy regulators 1-3. Arl6IP1 is an endoplasmic reticulum (ER) protein that has an important role in cell conduction and material transport. Arl6IP1, a tetraspan membrane protein, is an anti-apoptotic protein specific to multicellular organisms, and is a potential player in shaping the ER tubules in mammalian cells. In Drosophila, knockdown of the Arl6IP1 gene leads to progressive motor deficit. An Arl6IP1 variant has also been associated with hereditary spastic paraplegia (HSP), motor and sensory polyneuropathy, and acromutilation. Reticulophagy regulator 1 (RETREG1/FAM134B) is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. RETREG2/FAM134A and RETREG3/FAM134C has been shown to interact with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. Arl6IP1 shows some sequence similarity to the RHD of reticulophagy regulators, which may function in inducing membrane curvature.


Pssm-ID: 411696  Cd Length: 178  Bit Score: 157.99  E-value: 2.94e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425   4 RLRKW---SWEVINSKPDERPRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLL 80
Cdd:cd21102    64 RSNKStseVGFEFHPMLLSVPELCHNIAESWMSAVIFLLELLQLKEQNPGKFCLLVCVGLAVLAILGQYIPGVLLSYLIL 143

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1958752425  81 LFAFLCPLFKCNDIGQKIY---SKVKSILLKLDFG 112
Cdd:cd21102   144 TSLLLWPLLNYHGLIDKLYgmaKRLHPKLLKLDES 178
RETR3_RHD cd22562
N-terminal reticulon-homology domain of Reticulophagy regulator 3; Reticulophagy regulator 3 ...
 9-113 1.30e-32

N-terminal reticulon-homology domain of Reticulophagy regulator 3; Reticulophagy regulator 3 (RETR3 or RETREG3), also called FAM134C (family with sequence similarity 134, member C), mediates NRF1-enhanced neurite outgrowth. It interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. RETREG3/FAM134C contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an endoplasmic reticulum protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature.


Pssm-ID: 411701  Cd Length: 192  Bit Score: 120.23  E-value: 1.30e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425   9 SWEVINSKPDERPRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPL 88
Cdd:cd22562    86 SWGFVHPRLLSVPELCHHVAEVWVSGTNFLRNLLLFKKQNPGKFCLLVCGVLTFLAVLGRYIPGLLLSYLLLLFVLLWPL 165

                          90       100
                  ....*....|....*....|....*
gi 1958752425  89 FKCNDIGQKIYSKVKSILLKLDFGI 113
Cdd:cd22562   166 AVYHRLGQRIYVKLEPALQRLDFSV 190
RETR2_RHD cd22561
N-terminal reticulon-homology domain of Reticulophagy regulator 2; Reticulophagy regulator 2 ...
 21-111 2.08e-27

N-terminal reticulon-homology domain of Reticulophagy regulator 2; Reticulophagy regulator 2 (RETR2 or RETREG2), also called FAM134A (family with sequence similarity 134, member A), C2orf17, or MAG2, interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. RETREG2/FAM134A contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an endoplasmic reticulum protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature.


Pssm-ID: 411700  Cd Length: 199  Bit Score: 106.79  E-value: 2.08e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425  21 PRLSHCIAESWMNFSIFLQEMSLFKQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPLFKCNDIGQKIYS 100
Cdd:cd22561   105 PELCHYLAESWLTFQLYLQELLQYKRQNPGQFCARVCSGCAVLAVLGHYVPGIMISYIVLLSVLLWPLVVYHELIQRMYT 184

                          90
                  ....*....|.
gi 1958752425 101 KVKSILLKLDF 111
Cdd:cd22561   185 RLEPVLMKLDY 195
Arl6IP1 cd22559
ADP-ribosylation factor-like protein 6-interacting protein 1; ADP-ribosylation factor-like 6 ...
 45-109 8.35e-04

ADP-ribosylation factor-like protein 6-interacting protein 1; ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), also called apoptotic regulator in the membrane of the endoplasmic reticulum (ARMER), is an endoplasmic reticulum (ER) protein that has an important role in cell conduction and material transport. Arl6IP1, a tetraspan membrane protein, is an anti-apoptotic protein specific to multicellular organisms, and is a potential player in shaping the ER tubules in mammalian cells. In neurons, Arl6IP1 has been associated with the regulation of glutamate, a major excitatory neurotransmitter in excitatory synapses. In Drosophila, knockdown of the Arl6IP1 gene leads to progressive motor deficit. An Arl6IP1 variant has also been associated with hereditary spastic paraplegia (HSP), motor and sensory polyneuropathy, and acromutilation. Arl6IP1 shows some sequence similarity to the reticulon-homology domain (RHD) of reticulophagy regulators, which may function in inducing membrane curvature.


Pssm-ID: 411698  Cd Length: 167  Bit Score: 39.55  E-value: 8.35e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958752425  45 KQQSPGKFCLLVCSVCTFFTILGSYIPGVILSYLLLLFAFLCPLFKCNDIGQKIYSKVKSILLKL 109
Cdd:cd22559    97 KEEKPKMYFISVMGSLAAVAWIGNQVHNLLLTYLIVLFLLLLPGLKHHGILQKYIGMAKRVINKL 161
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 126-235 7.21e-03

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 38.34  E-value: 7.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958752425  126 EADKEKSHKDDSEIDFSALCPKISLTVAAKELS---VSDTDVSEVSWTDNGTFNLSEGYTPQTDTSDDLDRPSEEvfSRD 202
Cdd:TIGR00600  648 ESEKEESESDGSFIEVDSVSSTLELQVPSKSQPtdeSEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEE--EKD 725

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958752425  203 LSDFPSLENGAGTNDEDELS---LGLPTELKTKKQQ 235
Cdd:TIGR00600  726 ADDFKNEWQDISLEELEALEanlLAEQNSLKAQKQQ 761
 
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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