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Conserved domains on  [gi|1047225681|ref|NP_001316628|]
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AP-4 complex subunit sigma-1 isoform 3 [Mus musculus]

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 ...
 3-131 5.45e-62

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 cd14832:

Pssm-ID: 365781  Cd Length: 138  Bit Score: 186.67  E-value: 5.45e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   3 KFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYE 82
Cdd:cd14832     1 KFILMVNKQGQTRLAQYYEFLSIEERVALEGEIIRKCLSRSEKQCSFLEYRGYKLVYRRYASLYFIVGVDEDENELAILE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1047225681  83 FIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQGCSV 131
Cdd:cd14832    81 FIHNLVETLDKYFENVCELDIMF-------NLEKAHFILDEMVMNGCIV 122
 
Name Accession Description Interval E-value
AP4_sigma cd14832
AP-4 complex subunit sigma; AP-4 complex sigma subunit is part of the heterotetrameric adaptor ...
 3-131 5.45e-62

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: 186.67  E-value: 5.45e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   3 KFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYE 82
Cdd:cd14832     1 KFILMVNKQGQTRLAQYYEFLSIEERVALEGEIIRKCLSRSEKQCSFLEYRGYKLVYRRYASLYFIVGVDEDENELAILE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1047225681  83 FIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQGCSV 131
Cdd:cd14832    81 FIHNLVETLDKYFENVCELDIMF-------NLEKAHFILDEMVMNGCIV 122
APS2 COG5030
Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];
1-128 6.56e-39

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


Pssm-ID: 227363  Cd Length: 152  Bit Score: 128.68  E-value: 6.56e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   1 MIKFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAI 80
Cdd:COG5030     1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELII 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1047225681  81 YEFIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQG 128
Cdd:COG5030    81 LELIHNFVEILDRFFGNVCELDLIF-------NFQKVYAILDEMILGG 121
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
1-128 8.39e-33

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 112.84  E-value: 8.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   1 MIKFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAI 80
Cdd:pfam01217   1 MIKAILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPKMSNFIEFNDLKVIYKRYATLYFVVIVDDQDNELII 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1047225681  81 YEFIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQG 128
Cdd:pfam01217  81 LELIHRFVESLDRYFGNVCELDLIF-------NFEKVYLILDEMVMGG 121
 
Name Accession Description Interval E-value
AP4_sigma cd14832
AP-4 complex subunit sigma; AP-4 complex sigma subunit is part of the heterotetrameric adaptor ...
 3-131 5.45e-62

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: 186.67  E-value: 5.45e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   3 KFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYE 82
Cdd:cd14832     1 KFILMVNKQGQTRLAQYYEFLSIEERVALEGEIIRKCLSRSEKQCSFLEYRGYKLVYRRYASLYFIVGVDEDENELAILE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1047225681  83 FIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQGCSV 131
Cdd:cd14832    81 FIHNLVETLDKYFENVCELDIMF-------NLEKAHFILDEMVMNGCIV 122
AP2_sigma cd14833
AP-2 complex subunit sigma; AP-2 complex sigma subunit is part of the heterotetrameric adaptor ...
 1-105 1.30e-39

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: 130.00  E-value: 1.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   1 MIKFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAI 80
Cdd:cd14833     1 MIRFILIQNRQGKTRLAKWYVPYDDDEKQKLEEEVHRLVTSRDKKHTNFVEFRNYKLVYRRYAGLFFCICVDVNDNELAY 80

                          90       100
                  ....*....|....*....|....*
gi 1047225681  81 YEFIHNFVEVLDGYFSRVSELDVSF 105
Cdd:cd14833    81 LEAIHLFVEVLDEYFGNVCELDLVF 105
APS2 COG5030
Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];
1-128 6.56e-39

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


Pssm-ID: 227363  Cd Length: 152  Bit Score: 128.68  E-value: 6.56e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   1 MIKFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAI 80
Cdd:COG5030     1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELII 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1047225681  81 YEFIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQG 128
Cdd:COG5030    81 LELIHNFVEILDRFFGNVCELDLIF-------NFQKVYAILDEMILGG 121
AP_sigma cd14827
AP complex subunit sigma; AP complex sigma subunits are part of the heterotetrameric adaptor ...
 3-129 5.96e-37

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: 122.93  E-value: 5.96e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   3 KFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYE 82
Cdd:cd14827     1 RFILLFNRQGKTRLAKWYMQFDDDERQKLIEEIVQVVLSRDAKHCNFVEFRNYKLIYRRYASLYFCICVDSNDNELAILE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1047225681  83 FIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQGC 129
Cdd:cd14827    81 AIHNFVETLDKYFENVCELDLIF-------NFEKVYFIVDEMVLGGE 120
AP1_sigma cd14831
AP-1 complex subunit sigma; AP-1 complex sigma subunit is part of the heterotetrameric adaptor ...
 3-105 1.36e-35

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: 119.59  E-value: 1.36e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   3 KFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYE 82
Cdd:cd14831     1 HFLLLFSRQGKVRLSKWYSAYSQKEKAKITREVSTLVLARKPKMCNFLEWRDLKIVYKRYASLYFVCCVDKDDNELITLE 80

                          90       100
                  ....*....|....*....|...
gi 1047225681  83 FIHNFVEVLDGYFSRVSELDVSF 105
Cdd:cd14831    81 IIHRYVEILDKYFGNVCELDIIF 103
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
1-128 8.39e-33

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 112.84  E-value: 8.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   1 MIKFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAI 80
Cdd:pfam01217   1 MIKAILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPKMSNFIEFNDLKVIYKRYATLYFVVIVDDQDNELII 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1047225681  81 YEFIHNFVEVLDGYFSRVSELDVSFfctffhgMWQKAHSGCDHQVLQG 128
Cdd:pfam01217  81 LELIHRFVESLDRYFGNVCELDLIF-------NFEKVYLILDEMVMGG 121
AP3_sigma cd14834
AP-3 complex subunit sigma; AP-3 complex sigma subunit is part of the heterotetrameric adaptor ...
 1-118 8.33e-26

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: 94.99  E-value: 8.33e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   1 MIKFFLMVNKQGQTRLSKYYEHVDINKRALLETEVSKSCLSRSSEQCSFIEY------KDFKLIYRQYAALFVVVGVNDT 74
Cdd:cd14834     1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGgsliggSDTKLIYRHYATLYFVFCVDSS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1047225681  75 ENEMAIYEFIHNFVEVLDGYFSRVSELDVsffctFFHgmWQKAH 118
Cdd:cd14834    81 ESELGILDLIQVFVETLDKCFENVCELDL-----IFH--VDKVH 117
AP_longin-like cd14823
Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the ...
 3-107 1.37e-11

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: 57.91  E-value: 1.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047225681   3 KFFLMVNKQGQTRLSKYYEHvDINKRALLETEVSKSCLSRSSEQCSFIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYE 82
Cdd:cd14823     1 KAILVLDNDGKRLFAKYYDD-TYPSVKEQKAFEKNIFNKKHRTDSEIVLLEGLRVVYKSSIDLYFVVIGSKNENELLLLE 79

                          90       100
                  ....*....|....*....|....*
gi 1047225681  83 FIHNFVEVLDGYFSRVSELDVSFFC 107
Cdd:cd14823    80 VLNCLVDVLSEYFRKVEERAILENF 104
AP_Mu_N cd14828
AP complex subunit mu N-terminal domain; AP complex mu subunits are part of the ...
 49-102 6.35e-03

AP complex subunit mu N-terminal domain; AP complex mu 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 mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal.


Pssm-ID: 341432  Cd Length: 136  Bit Score: 34.48  E-value: 6.35e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1047225681  49 FIEYKDFKLIYRQYAALFVVVGVNDTENEMAIYEFIHNFVEVLDGYFsRVSELD 102
Cdd:cd14828    46 IISSNGWNFIYIKRDDLYFVSVTQTNVNLMSVLVFLDQFYDLLKDYF-GVKKLD 98
 
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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