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Conserved domains on  [gi|1907173682|ref|XP_036008240|]
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syndetin isoform X1 [Mus musculus]

Protein Classification

syndetin( domain architecture ID 10996518)

syndetin acts as component of the EARP complex that is involved in endocytic recycling

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF2451 pfam10474
Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its ...
 454-688 7.07e-126

Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2450.


:

Pssm-ID: 463103  Cd Length: 229  Bit Score: 372.68  E-value: 7.07e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907173682 454 LYGLAERVVATESLVFLAEQFEFLQPHLDAVMPAVKKPFLQQFYSQTVSTASELRKPIYWIVAGKAIDYEQMLLLMMNVK 533
Cdd:pfam10474   1 LYGLKERIIAVESLVFLAEQLRSLKPYLESLLPSNKKDLLEQFYSQTVSIVPDLREPIYKTVASRLLDLEQILNLIANVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907173682 534 WDVKEIMSQHNIYVDALLKEFEQFNKRLNEVskrvRIPLPVSNILWEHCIRLANRTIVEGYANVKKCSNEGRALMQLDFQ 613
Cdd:pfam10474  81 WDVKEIMSQHNPYVDLLLQEFQKFAKRLDEA----RIPEEVKNLLWESAIEYANETLVEGFSRVKKCSNEGRALMQLDFQ 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907173682 614 QFLMKLEKLTDIRPIPDKEFVETYIKAYYLTENDMERWIKEHREYSTKQLTNLVNVClgSHINKKARQKLLAAID 688
Cdd:pfam10474 157 QLLNKLEKLTPIKPIPHREYVENYIKAYYLPEDELEEWIREHPEYSKKQLISLVNCV--AHLKKKTRQRLLNALE 229
COG2 super family cl19297
COG (conserved oligomeric Golgi) complex component, COG2; The COG complex comprises eight ...
 1-76 1.76e-27

COG (conserved oligomeric Golgi) complex component, COG2; The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs.


The actual alignment was detected with superfamily member pfam10475:

Pssm-ID: 473160  Cd Length: 291  Bit Score: 112.84  E-value: 1.76e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907173682   1 MDQLHMHFTQAIHNTVFQVVLGYVELCAGNtDTKFQKLQYKDLCTHVTPDSYIPCLADLCKALWEVMLSYYRTMEW 76
Cdd:pfam10475 217 ADKLHSNFVQAIESTTFAVLKSHLELTYSN-PERLKKLTYKDLCLQLPEDQYVPCLLELCEVLWDLMASYYQIMQW 291
 
Name Accession Description Interval E-value
DUF2451 pfam10474
Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its ...
 454-688 7.07e-126

Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2450.


Pssm-ID: 463103  Cd Length: 229  Bit Score: 372.68  E-value: 7.07e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907173682 454 LYGLAERVVATESLVFLAEQFEFLQPHLDAVMPAVKKPFLQQFYSQTVSTASELRKPIYWIVAGKAIDYEQMLLLMMNVK 533
Cdd:pfam10474   1 LYGLKERIIAVESLVFLAEQLRSLKPYLESLLPSNKKDLLEQFYSQTVSIVPDLREPIYKTVASRLLDLEQILNLIANVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907173682 534 WDVKEIMSQHNIYVDALLKEFEQFNKRLNEVskrvRIPLPVSNILWEHCIRLANRTIVEGYANVKKCSNEGRALMQLDFQ 613
Cdd:pfam10474  81 WDVKEIMSQHNPYVDLLLQEFQKFAKRLDEA----RIPEEVKNLLWESAIEYANETLVEGFSRVKKCSNEGRALMQLDFQ 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907173682 614 QFLMKLEKLTDIRPIPDKEFVETYIKAYYLTENDMERWIKEHREYSTKQLTNLVNVClgSHINKKARQKLLAAID 688
Cdd:pfam10474 157 QLLNKLEKLTPIKPIPHREYVENYIKAYYLPEDELEEWIREHPEYSKKQLISLVNCV--AHLKKKTRQRLLNALE 229
Vps54_N pfam10475
Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, ...
 1-76 1.76e-27

Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, pfam07928, brings about localization to an early endocytic compartment.


Pssm-ID: 431303  Cd Length: 291  Bit Score: 112.84  E-value: 1.76e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907173682   1 MDQLHMHFTQAIHNTVFQVVLGYVELCAGNtDTKFQKLQYKDLCTHVTPDSYIPCLADLCKALWEVMLSYYRTMEW 76
Cdd:pfam10475 217 ADKLHSNFVQAIESTTFAVLKSHLELTYSN-PERLKKLTYKDLCLQLPEDQYVPCLLELCEVLWDLMASYYQIMQW 291
 
Name Accession Description Interval E-value
DUF2451 pfam10474
Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its ...
 454-688 7.07e-126

Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2450.


Pssm-ID: 463103  Cd Length: 229  Bit Score: 372.68  E-value: 7.07e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907173682 454 LYGLAERVVATESLVFLAEQFEFLQPHLDAVMPAVKKPFLQQFYSQTVSTASELRKPIYWIVAGKAIDYEQMLLLMMNVK 533
Cdd:pfam10474   1 LYGLKERIIAVESLVFLAEQLRSLKPYLESLLPSNKKDLLEQFYSQTVSIVPDLREPIYKTVASRLLDLEQILNLIANVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907173682 534 WDVKEIMSQHNIYVDALLKEFEQFNKRLNEVskrvRIPLPVSNILWEHCIRLANRTIVEGYANVKKCSNEGRALMQLDFQ 613
Cdd:pfam10474  81 WDVKEIMSQHNPYVDLLLQEFQKFAKRLDEA----RIPEEVKNLLWESAIEYANETLVEGFSRVKKCSNEGRALMQLDFQ 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907173682 614 QFLMKLEKLTDIRPIPDKEFVETYIKAYYLTENDMERWIKEHREYSTKQLTNLVNVClgSHINKKARQKLLAAID 688
Cdd:pfam10474 157 QLLNKLEKLTPIKPIPHREYVENYIKAYYLPEDELEEWIREHPEYSKKQLISLVNCV--AHLKKKTRQRLLNALE 229
Vps54_N pfam10475
Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, ...
 1-76 1.76e-27

Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, pfam07928, brings about localization to an early endocytic compartment.


Pssm-ID: 431303  Cd Length: 291  Bit Score: 112.84  E-value: 1.76e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907173682   1 MDQLHMHFTQAIHNTVFQVVLGYVELCAGNtDTKFQKLQYKDLCTHVTPDSYIPCLADLCKALWEVMLSYYRTMEW 76
Cdd:pfam10475 217 ADKLHSNFVQAIESTTFAVLKSHLELTYSN-PERLKKLTYKDLCLQLPEDQYVPCLLELCEVLWDLMASYYQIMQW 291
 
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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