NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958789950|ref|XP_038935278|]
View 

coatomer subunit zeta-1 isoform X2 [Rattus norvegicus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 14-87 4.47e-32

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 cd14829:

Pssm-ID: 365781  Cd Length: 132  Bit Score: 109.94  E-value: 4.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950  14 KAILILDNDGDRLFAK----------------------------------------------------------LMLMAV 35
Cdd:cd14829     1 KAILILDNDGKRVLAKyyddtfptvkeqkafekklfdkthkanaeiilldgltvvyksnidltfyvvgssdeneLILASV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958789950  36 LNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHR 87
Cdd:cd14829    81 LNCLYDALSLLLRKNVEKRALLENLDLVLLALDEIVDGGIILETDPTAIASR 132
 
Name Accession Description Interval E-value
Zeta-COP cd14829
zeta subunit of the F-COPI complex; Zeta subunit of the heterotetrameric F-COPI complex, which ...
 14-87 4.47e-32

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: 109.94  E-value: 4.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950  14 KAILILDNDGDRLFAK----------------------------------------------------------LMLMAV 35
Cdd:cd14829     1 KAILILDNDGKRVLAKyyddtfptvkeqkafekklfdkthkanaeiilldgltvvyksnidltfyvvgssdeneLILASV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958789950  36 LNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHR 87
Cdd:cd14829    81 LNCLYDALSLLLRKNVEKRALLENLDLVLLALDEIVDGGIILETDPTAIASR 132
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
9-95 5.88e-22

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 84.33  E-value: 5.88e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950   9 SLYTVKAILILDNDgdrlfakLMLMAVLNCLFDSLSQMLRkNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHRV 88
Cdd:pfam01217  64 TLYFVVIVDDQDNE-------LIILELIHRFVESLDRYFG-NVCELDLIFNFEKVYLILDEMVMGGEILETSKNEVLHRV 135


                  ....*..
gi 1958789950  89 ALRGEDV 95
Cdd:pfam01217 136 ALLDELA 142
RET3 COG5541
Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, ...
 29-88 3.47e-06

Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227828  Cd Length: 187  Bit Score: 43.78  E-value: 3.47e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950  29 KLMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHRV 88
Cdd:COG5541    91 EPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRV 150
 
Name Accession Description Interval E-value
Zeta-COP cd14829
zeta subunit of the F-COPI complex; Zeta subunit of the heterotetrameric F-COPI complex, which ...
 14-87 4.47e-32

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: 109.94  E-value: 4.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950  14 KAILILDNDGDRLFAK----------------------------------------------------------LMLMAV 35
Cdd:cd14829     1 KAILILDNDGKRVLAKyyddtfptvkeqkafekklfdkthkanaeiilldgltvvyksnidltfyvvgssdeneLILASV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958789950  36 LNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHR 87
Cdd:cd14829    81 LNCLYDALSLLLRKNVEKRALLENLDLVLLALDEIVDGGIILETDPTAIASR 132
Clat_adaptor_s pfam01217
Clathrin adaptor complex small chain;
9-95 5.88e-22

Clathrin adaptor complex small chain;


Pssm-ID: 460115  Cd Length: 142  Bit Score: 84.33  E-value: 5.88e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950   9 SLYTVKAILILDNDgdrlfakLMLMAVLNCLFDSLSQMLRkNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHRV 88
Cdd:pfam01217  64 TLYFVVIVDDQDNE-------LIILELIHRFVESLDRYFG-NVCELDLIFNFEKVYLILDEMVMGGEILETSKNEVLHRV 135


                  ....*..
gi 1958789950  89 ALRGEDV 95
Cdd:pfam01217 136 ALLDELA 142
AP_longin-like cd14823
Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the ...
 30-87 3.75e-20

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: 79.48  E-value: 3.75e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958789950  30 LMLMAVLNCLFDSLSQMLRkNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHR 87
Cdd:cd14823    75 LLLLEVLNCLVDVLSEYFR-KVEERAILENFEGLYFALDEIVDGGYIQETDPKQVVHF 131
longin-like cd14818
Longin-like domains; Longin-like domains are small protein domains present in a variety of ...
 23-70 8.62e-10

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).


Pssm-ID: 341426  Cd Length: 117  Bit Score: 52.14  E-value: 8.62e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958789950  23 GDRLFAKLMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEI 70
Cdd:cd14818    70 TDEQELRQELFQTLNLLLKEFNSLHGSEVITKNIEDDLEEFESYLDIK 117
RET3 COG5541
Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, ...
 29-88 3.47e-06

Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227828  Cd Length: 187  Bit Score: 43.78  E-value: 3.47e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958789950  29 KLMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHRV 88
Cdd:COG5541    91 EPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRV 150
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH