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Conserved domains on  [gi|1396658779|ref|NP_001351051|]
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AP-3 complex subunit sigma-1 isoform 9 [Homo sapiens]

Protein Classification

longin-like domain-containing protein( domain architecture ID 1000061)

longin-like domain-containing protein; longin-like domains are small protein domains present in a variety of proteins and members of protein complexes involved in or required for different steps during the transport of proteins from the ribosome to the ER to the plasma membrane, via the Golgi apparatus

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
longin-like super family cl38905
Longin-like domains; Longin-like domains are small protein domains present in a variety of ...
 1-91 3.91e-70

Longin-like domains; Longin-like domains are small protein domains present in a variety of proteins and members of protein complexes involved in or required for different steps during the transport of proteins from the ribosome to the ER to the plasma membrane, via the Golgi apparatus. Examples are mu and sigma subunits of the heterotetrameric adaptor protein (AP) complex, zeta and delta subunits of the heterotetrameric F-COPI complex, a subgroup of R-SNARE proteins, a subfamily of the transport protein particle (TRAPP), and the signal recognition particle receptor subunit alpha (SR-alpha).


The actual alignment was detected with superfamily member cd14834:

Pssm-ID: 365781  Cd Length: 146  Bit Score: 207.08  E-value: 3.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:cd14834     1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGGSLIGGSDTKLIYRHYATLYFVFCVDSS 80

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:cd14834    81 ESELGILDLIQ 91
 
Name Accession Description Interval E-value
AP3_sigma cd14834
AP-3 complex subunit sigma; AP-3 complex sigma subunit is part of the heterotetrameric adaptor ...
 1-91 3.91e-70

AP-3 complex subunit sigma; AP-3 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large delta-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-3 binds the coat protein clathrin and the phospholipid PI(3)P and it is localized in the endosome. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341438  Cd Length: 146  Bit Score: 207.08  E-value: 3.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:cd14834     1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGGSLIGGSDTKLIYRHYATLYFVFCVDSS 80

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:cd14834    81 ESELGILDLIQ 91
APS2 COG5030
Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];
1-91 1.75e-33

Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];


Pssm-ID: 227363  Cd Length: 152  Bit Score: 114.43  E-value: 1.75e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEgglligGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:COG5030     1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIE------GKNEKIVYRRYATLYFVFGVDND 74

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:COG5030    75 DNELIILELIH 85
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
1-91 1.45e-31

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 109.37  E-value: 1.45e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEgglligGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:pfam01217   1 MIKAILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPKMSNFIE------FNDLKVIYKRYATLYFVVIVDDQ 74

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:pfam01217  75 DNELIILELIH 85
 
Name Accession Description Interval E-value
AP3_sigma cd14834
AP-3 complex subunit sigma; AP-3 complex sigma subunit is part of the heterotetrameric adaptor ...
 1-91 3.91e-70

AP-3 complex subunit sigma; AP-3 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large delta-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-3 binds the coat protein clathrin and the phospholipid PI(3)P and it is localized in the endosome. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341438  Cd Length: 146  Bit Score: 207.08  E-value: 3.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:cd14834     1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGGSLIGGSDTKLIYRHYATLYFVFCVDSS 80

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:cd14834    81 ESELGILDLIQ 91
AP_sigma cd14827
AP complex subunit sigma; AP complex sigma subunits are part of the heterotetrameric adaptor ...
 3-91 2.23e-38

AP complex subunit sigma; AP complex sigma subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341431  Cd Length: 138  Bit Score: 126.40  E-value: 2.23e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   3 KAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGlliggsDNKLIYRHYATLYFVFCVDSSES 82
Cdd:cd14827     1 RFILLFNRQGKTRLAKWYMQFDDDERQKLIEEIVQVVLSRDAKHCNFVEFR------NYKLIYRRYASLYFCICVDSNDN 74


                  ....*....
gi 1396658779  83 ELGILDLIQ 91
Cdd:cd14827    75 ELAILEAIH 83
APS2 COG5030
Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];
1-91 1.75e-33

Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];


Pssm-ID: 227363  Cd Length: 152  Bit Score: 114.43  E-value: 1.75e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEgglligGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:COG5030     1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIE------GKNEKIVYRRYATLYFVFGVDND 74

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:COG5030    75 DNELIILELIH 85
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
1-91 1.45e-31

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 109.37  E-value: 1.45e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEgglligGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:pfam01217   1 MIKAILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPKMSNFIE------FNDLKVIYKRYATLYFVVIVDDQ 74

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:pfam01217  75 DNELIILELIH 85
AP2_sigma cd14833
AP-2 complex subunit sigma; AP-2 complex sigma subunit is part of the heterotetrameric adaptor ...
 1-91 1.63e-26

AP-2 complex subunit sigma; AP-2 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-2 complex which consists of one large alpha-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-2 the coat protein is clathrin. AP-2 binds the phospholipid PI(4,5)P2 which is important for its localisation to the plasma membrane. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341437  Cd Length: 141  Bit Score: 96.10  E-value: 1.63e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   1 MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEgglligGSDNKLIYRHYATLYFVFCVDSS 80
Cdd:cd14833     1 MIRFILIQNRQGKTRLAKWYVPYDDDEKQKLEEEVHRLVTSRDKKHTNFVE------FRNYKLVYRRYAGLFFCICVDVN 74

                          90
                  ....*....|.
gi 1396658779  81 ESELGILDLIQ 91
Cdd:cd14833    75 DNELAYLEAIH 85
AP1_sigma cd14831
AP-1 complex subunit sigma; AP-1 complex sigma subunit is part of the heterotetrameric adaptor ...
 5-91 2.82e-24

AP-1 complex subunit sigma; AP-1 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large gamma-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-1 the coat protein is clathrin. AP-1 binds the phospholipid PI(4)P which plays a role in its localisation to the trans-Golgi network (TGN)/endosome. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341435  Cd Length: 143  Bit Score: 90.70  E-value: 2.82e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   5 ILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEgglligGSDNKLIYRHYATLYFVFCVDSSESEL 84
Cdd:cd14831     3 LLLFSRQGKVRLSKWYSAYSQKEKAKITREVSTLVLARKPKMCNFLE------WRDLKIVYKRYASLYFVCCVDKDDNEL 76


                  ....*..
gi 1396658779  85 GILDLIQ 91
Cdd:cd14831    77 ITLEIIH 83
AP4_sigma cd14832
AP-4 complex subunit sigma; AP-4 complex sigma subunit is part of the heterotetrameric adaptor ...
 3-92 3.35e-16

AP-4 complex subunit sigma; AP-4 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large epsilon-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-4 does not bind the coat protein clathrin, it is associated with nonclathrin coats. Its phospholipid binding partner is unknown and it is localized in the trans-Golgi network (TGN). The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341436  Cd Length: 138  Bit Score: 69.57  E-value: 3.35e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   3 KAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGglliggSDNKLIYRHYATLYFVFCVDSSES 82
Cdd:cd14832     1 KFILMVNKQGQTRLAQYYEFLSIEERVALEGEIIRKCLSRSEKQCSFLEY------RGYKLVYRRYASLYFIVGVDEDEN 74

                          90
                  ....*....|
gi 1396658779  83 ELGILDLIQA 92
Cdd:cd14832    75 ELAILEFIHN 84
AP_longin-like cd14823
Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the ...
 3-90 2.00e-03

Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals.


Pssm-ID: 341427  Cd Length: 131  Bit Score: 35.96  E-value: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1396658779   3 KAILIFNNHGKPRLSKFYQPySEDTQQQIIRETFHLVSKRDENVCNFLEGGLLiggsdnKLIYRHYATLYFVFCVDSSES 82
Cdd:cd14823     1 KAILVLDNDGKRLFAKYYDD-TYPSVKEQKAFEKNIFNKKHRTDSEIVLLEGL------RVVYKSSIDLYFVVIGSKNEN 73


                  ....*...
gi 1396658779  83 ELGILDLI 90
Cdd:cd14823    74 ELLLLEVL 81
 
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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