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Conserved domains on  [gi|670434930|ref|XP_008658025|]
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AP-3 complex subunit sigma-2 isoform X1 [Zea mays]

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 ...
 1-149 1.21e-74

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: 220.18  E-value: 1.21e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDSIF-GPGTKMVYKHLATLYFVFVFDSS 79
Cdd:cd14834    1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGGSLIgGSDTKLIYRHYATLYFVFCVDSS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930  80 ENELAMLDLVQVFVETLDRCFKNVCELDIVFNFNkaaeKLHTILDEMISGGQVIETSSEQIMKSVEEIER 149
Cdd:cd14834   81 ESELGILDLIQVFVETLDKCFENVCELDLIFHVD----KVHYILDEIVMGGMVLETNMTEILTAIEEQNK 146
 
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 ...
 1-149 1.21e-74

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: 220.18  E-value: 1.21e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDSIF-GPGTKMVYKHLATLYFVFVFDSS 79
Cdd:cd14834    1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGGSLIgGSDTKLIYRHYATLYFVFCVDSS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930  80 ENELAMLDLVQVFVETLDRCFKNVCELDIVFNFNkaaeKLHTILDEMISGGQVIETSSEQIMKSVEEIER 149
Cdd:cd14834   81 ESELGILDLIQVFVETLDKCFENVCELDLIFHVD----KVHYILDEIVMGGMVLETNMTEILTAIEEQNK 146
APS2 COG5030
Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];
1-156 2.04e-48

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


Pssm-ID: 227363  Cd Length: 152  Bit Score: 153.72  E-value: 2.04e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKvdsifGPGTKMVYKHLATLYFVFVFDSSE 80
Cdd:COG5030    1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIE-----GKNEKIVYRRYATLYFVFGVDNDD 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 670434930  81 NELAMLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMKSVEEIERLEKQSST 156
Cdd:COG5030   76 NELIILELIHNFVEILDRFFGNVCELDLIFNF----QKVYAILDEMILGGEIIESSKNEVLEHVYALDAESTDDKI 147
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
1-151 2.78e-46

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 147.89  E-value: 2.78e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930    1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDsifgpGTKMVYKHLATLYFVFVFDSSE 80
Cdd:pfam01217   1 MIKAILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPKMSNFIEFN-----DLKVIYKRYATLYFVVIVDDQD 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 670434930   81 NELAMLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMKSVEEIERLE 151
Cdd:pfam01217  76 NELIILELIHRFVESLDRYFGNVCELDLIFNF----EKVYLILDEMVMGGEILETSKNEVLHRVALLDELA 142
 
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 ...
 1-149 1.21e-74

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: 220.18  E-value: 1.21e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDSIF-GPGTKMVYKHLATLYFVFVFDSS 79
Cdd:cd14834    1 MIKAILIFNNHGKPRLSKFYQHYSEEKQQQIIRETFQLVSKRDDNVCNFLEGGSLIgGSDTKLIYRHYATLYFVFCVDSS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930  80 ENELAMLDLVQVFVETLDRCFKNVCELDIVFNFNkaaeKLHTILDEMISGGQVIETSSEQIMKSVEEIER 149
Cdd:cd14834   81 ESELGILDLIQVFVETLDKCFENVCELDLIFHVD----KVHYILDEIVMGGMVLETNMTEILTAIEEQNK 146
APS2 COG5030
Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion];
1-156 2.04e-48

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


Pssm-ID: 227363  Cd Length: 152  Bit Score: 153.72  E-value: 2.04e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKvdsifGPGTKMVYKHLATLYFVFVFDSSE 80
Cdd:COG5030    1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIE-----GKNEKIVYRRYATLYFVFGVDNDD 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 670434930  81 NELAMLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMKSVEEIERLEKQSST 156
Cdd:COG5030   76 NELIILELIHNFVEILDRFFGNVCELDLIFNF----QKVYAILDEMILGGEIIESSKNEVLEHVYALDAESTDDKI 147
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
1-151 2.78e-46

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 147.89  E-value: 2.78e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930    1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDsifgpGTKMVYKHLATLYFVFVFDSSE 80
Cdd:pfam01217   1 MIKAILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPKMSNFIEFN-----DLKVIYKRYATLYFVVIVDDQD 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 670434930   81 NELAMLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMKSVEEIERLE 151
Cdd:pfam01217  76 NELIILELIHRFVESLDRYFGNVCELDLIFNF----EKVYLILDEMVMGGEILETSKNEVLHRVALLDELA 142
AP_sigma cd14827
AP complex subunit sigma; AP complex sigma subunits are part of the heterotetrameric adaptor ...
 3-145 3.29e-43

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: 140.27  E-value: 3.29e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   3 QAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKvdsifGPGTKMVYKHLATLYFVFVFDSSENE 82
Cdd:cd14827    1 RFILLFNRQGKTRLAKWYMQFDDDERQKLIEEIVQVVLSRDAKHCNFVE-----FRNYKLIYRRYASLYFCICVDSNDNE 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 670434930  83 LAMLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMKSVE 145
Cdd:cd14827   76 LAILEAIHNFVETLDKYFENVCELDLIFNF----EKVYFIVDEMVLGGEIRETSQTKILKQIE 134
AP1_sigma cd14831
AP-1 complex subunit sigma; AP-1 complex sigma subunit is part of the heterotetrameric adaptor ...
 5-154 6.66e-40

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: 131.91  E-value: 6.66e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   5 VMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDsifgpGTKMVYKHLATLYFVFVFDSSENELA 84
Cdd:cd14831    3 LLLFSRQGKVRLSKWYSAYSQKEKAKITREVSTLVLARKPKMCNFLEWR-----DLKIVYKRYASLYFVCCVDKDDNELI 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930  85 MLDLVQVFVETLDRCFKNVCELDIVFNFNKAaeklHTILDEMISGGQVIETSSEQIMKSVEEIERLEKQS 154
Cdd:cd14831   78 TLEIIHRYVEILDKYFGNVCELDIIFNFHKA----YFILDELLLGGELQETSKKNVLRAIEAQDLLQEEE 143
AP2_sigma cd14833
AP-2 complex subunit sigma; AP-2 complex sigma subunit is part of the heterotetrameric adaptor ...
 1-150 8.43e-40

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: 131.54  E-value: 8.43e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   1 MIQAVMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDSifgpgTKMVYKHLATLYFVFVFDSSE 80
Cdd:cd14833    1 MIRFILIQNRQGKTRLAKWYVPYDDDEKQKLEEEVHRLVTSRDKKHTNFVEFRN-----YKLVYRRYAGLFFCICVDVND 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930  81 NELAMLDLVQVFVETLDRCFKNVCELDIVFNFNkaaeKLHTILDEMISGGQVIETSSEQIMKSVEEIERL 150
Cdd:cd14833   76 NELAYLEAIHLFVEVLDEYFGNVCELDLVFNFY----KVYAILDEMFLAGEIQETSKKVILERLKELDKL 141
AP4_sigma cd14832
AP-4 complex subunit sigma; AP-4 complex sigma subunit is part of the heterotetrameric adaptor ...
 5-149 5.16e-32

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: 111.56  E-value: 5.16e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   5 VMVISTQAKPRLLKFYSFQPPEKHQDLVRCVFQLLSARPESASNFVKVDsifgpGTKMVYKHLATLYFVFVFDSSENELA 84
Cdd:cd14832    3 ILMVNKQGQTRLAQYYEFLSIEERVALEGEIIRKCLSRSEKQCSFLEYR-----GYKLVYRRYASLYFIVGVDEDENELA 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 670434930  85 MLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMKSVEEIER 149
Cdd:cd14832   78 ILEFIHNLVETLDKYFENVCELDIMFNL----EKAHFILDEMVMNGCIVETNKSNILAPILLMDK 138
AP_longin-like cd14823
Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the ...
 4-142 7.58e-18

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: 74.86  E-value: 7.58e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930   4 AVMVISTQAKPRLLKFYSFQPPEKhQDLVRCVFQLLSARPESASNFVKVDSIfgpgtKMVYKHLATLYFVFVFDSSENEL 83
Cdd:cd14823    2 AILVLDNDGKRLFAKYYDDTYPSV-KEQKAFEKNIFNKKHRTDSEIVLLEGL-----RVVYKSSIDLYFVVIGSKNENEL 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 670434930  84 AMLDLVQVFVETLDRCFKNVCELDIVFNFnkaaEKLHTILDEMISGGQVIETSSEQIMK 142
Cdd:cd14823   76 LLLEVLNCLVDVLSEYFRKVEERAILENF----EGLYFALDEIVDGGYIQETDPKQVVH 130
Zeta-COP cd14829
zeta subunit of the F-COPI complex; Zeta subunit of the heterotetrameric F-COPI complex, which ...
 63-141 9.22e-06

zeta subunit of the F-COPI complex; Zeta subunit of the heterotetrameric F-COPI complex, which consists of one beta-, one gamma-, one delta-, and one zeta subunit, where beta- and gamma- subunits are related to the large adaptor protein (AP) complex subunits, and delta- and zeta- subunits are related to the medium and small AP subunits, respectively. F-COPI forms a coatomer together with the B-COPI subcomplex, which assembles with a small GTPase, ADP-ribosylation factor 1 (ARF1), playing an important role in the formation of COPI complex-coated vesicles. COPI complex-coated vesicles function in the early secretory pathway mediating the retrograde transport from the Golgi to the ER, and intra-Golgi transport.


Pssm-ID: 341433  Cd Length: 132  Bit Score: 42.92  E-value: 9.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670434930  63 VYKHLATLYFVFVFDSSENELAMLDLVQVFVETLDRCFKNVCE-------LDIVFnfnkaaeklhTILDEMISGGQVIET 135
Cdd:cd14829   55 VYKSNIDLTFYVVGSSDENELILASVLNCLYDALSLLLRKNVEkrallenLDLVL----------LALDEIVDGGIILET 124


                 ....*.
gi 670434930 136 SSEQIM 141
Cdd:cd14829  125 DPTAIA 130
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
107-166 4.12e-03

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 36.92  E-value: 4.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 670434930 107 DIVFNFNKAAEKLHTILDEMISGGQVIETSSEQIMKSVEEI-ERLEKQSSTTSFIPKSITE 166
Cdd:COG0840  239 QLADAFNRMIENLRELVGQVRESAEQVASASEELAASAEELaAGAEEQAASLEETAAAMEE 299
 
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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