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Conserved domains on  [gi|1393428100|ref|NP_001350607|]
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synaptobrevin homolog YKT6 isoform 2 [Homo sapiens]

Protein Classification

longin domain-containing protein( domain architecture ID 13000503)

longin domain-containing protein similar to R-SNARE subgroup proteins, including VAMP7, Ykt6, and Sec22 which is required for transporting proteins from 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 cd14824
longin domain; Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including ...
 4-130 2.69e-29

longin domain; Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including VAMP7, Ykt6, and Sec22. Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain.


:

Pssm-ID: 341428  Cd Length: 122  Bit Score: 103.87  E-value: 2.69e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393428100   4 YSLSVLYKGEAkvVLLKAAYDVSSFSFfqrssVQEFMTFTSQLIVERSSK-GTRASVKEQDYLCHVYVRnDSLAGVVIAD 82
Cdd:cd14824     1 LYALIARGSDG--LILAEYTDLSSFSS-----VKENFKFVAKTILERTPPsGQRQSVEEGDYVFHYLVE-DGLCYLCITD 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1393428100  83 NEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPA--TIHYPALDGHLSRY 130
Cdd:cd14824    73 KEYPKRVAFAFLEEVLDEFLSKYGSSAWTAARPYlfSEFDPELKKLMKKY 122
SNARE super family cl22856
SNARE motif; SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) ...
 136-153 1.64e-06

SNARE motif; SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, Qb- and Qc-SNAREs are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles.


The actual alignment was detected with superfamily member cd15867:

Pssm-ID: 473982  Cd Length: 61  Bit Score: 43.13  E-value: 1.64e-06
                          10
                  ....*....|....*...
gi 1393428100 136 ADPMTKVQAELDETKIIL 153
Cdd:cd15867     1 ADKIMKVQSELDETKIIL 18
 
Name Accession Description Interval E-value
Longin cd14824
longin domain; Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including ...
 4-130 2.69e-29

longin domain; Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including VAMP7, Ykt6, and Sec22. Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain.


Pssm-ID: 341428  Cd Length: 122  Bit Score: 103.87  E-value: 2.69e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393428100   4 YSLSVLYKGEAkvVLLKAAYDVSSFSFfqrssVQEFMTFTSQLIVERSSK-GTRASVKEQDYLCHVYVRnDSLAGVVIAD 82
Cdd:cd14824     1 LYALIARGSDG--LILAEYTDLSSFSS-----VKENFKFVAKTILERTPPsGQRQSVEEGDYVFHYLVE-DGLCYLCITD 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1393428100  83 NEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPA--TIHYPALDGHLSRY 130
Cdd:cd14824    73 KEYPKRVAFAFLEEVLDEFLSKYGSSAWTAARPYlfSEFDPELKKLMKKY 122
Longin pfam13774
Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for ...
 44-115 2.24e-19

Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain.


Pssm-ID: 463978  Cd Length: 81  Bit Score: 77.19  E-value: 2.24e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1393428100  44 SQLIVER-SSKGTRASVKEQDYLCHVYVRNDsLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSP 115
Cdd:pfam13774   1 AKTILEKiPQNPQRQTYEGDNYTFHYLIEDG-LTYLVIADKSYPRRLAFAFLEEIKDEFLSTYGPWTASALRP 72
SNC1 COG5143
Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion];
3-155 5.14e-18

Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion];


Pssm-ID: 227472 [Multi-domain]  Cd Length: 190  Bit Score: 76.70  E-value: 5.14e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393428100   3 LYSLSVLYKGEAKVVLLKAAYDVSSFSFFQRSSVQEFMTFTSQliversSKGTRASVKEQDYLCHVYVRNDSLAGVVIAD 82
Cdd:COG5143     1 IASISLFRVKGEPLRTLSDAESLSSFSFFHRSKVKEVLRFLSK------TSASRASIESGDYFFHYLKMSSGIVYVPISD 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1393428100  83 NEYPSRVAFTLLEKVLDEFSKQVDRIDWpVGSPATIHYPALDGHLSR-YQNPREADPMTKVQAELDETKIILAR 155
Cdd:COG5143    75 KEYPNKLAYGYLNSIATEFLKSSALEQL-IDDTVGIMRVNIDKVIEKgYRDPSIQDKLDQLQQELEETKRVLNK 147
R-SNARE_YKT6 cd15867
SNARE motif of YKT6; Ykt6 forms complexes with syntaxin-5 (Qa), GS28 (Qb) and either Bet1 (Qc) ...
 136-153 1.64e-06

SNARE motif of YKT6; Ykt6 forms complexes with syntaxin-5 (Qa), GS28 (Qb) and either Bet1 (Qc) or GS15 (Qc). This complex regulates the early secretory pathway of eukaryotic cells at the level of the transport from the ER-Golgi intermediate compartment (ERGIC) to the cis-Golgi and transport from the trans-Golgi network to the cis-Golgi, respectively. Ykt6 is a member of the R-SNARE subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles.


Pssm-ID: 277220  Cd Length: 61  Bit Score: 43.13  E-value: 1.64e-06
                          10
                  ....*....|....*...
gi 1393428100 136 ADPMTKVQAELDETKIIL 153
Cdd:cd15867     1 ADKIMKVQSELDETKIIL 18
 
Name Accession Description Interval E-value
Longin cd14824
longin domain; Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including ...
 4-130 2.69e-29

longin domain; Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including VAMP7, Ykt6, and Sec22. Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain.


Pssm-ID: 341428  Cd Length: 122  Bit Score: 103.87  E-value: 2.69e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393428100   4 YSLSVLYKGEAkvVLLKAAYDVSSFSFfqrssVQEFMTFTSQLIVERSSK-GTRASVKEQDYLCHVYVRnDSLAGVVIAD 82
Cdd:cd14824     1 LYALIARGSDG--LILAEYTDLSSFSS-----VKENFKFVAKTILERTPPsGQRQSVEEGDYVFHYLVE-DGLCYLCITD 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1393428100  83 NEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPA--TIHYPALDGHLSRY 130
Cdd:cd14824    73 KEYPKRVAFAFLEEVLDEFLSKYGSSAWTAARPYlfSEFDPELKKLMKKY 122
Longin pfam13774
Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for ...
 44-115 2.24e-19

Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain.


Pssm-ID: 463978  Cd Length: 81  Bit Score: 77.19  E-value: 2.24e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1393428100  44 SQLIVER-SSKGTRASVKEQDYLCHVYVRNDsLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSP 115
Cdd:pfam13774   1 AKTILEKiPQNPQRQTYEGDNYTFHYLIEDG-LTYLVIADKSYPRRLAFAFLEEIKDEFLSTYGPWTASALRP 72
SNC1 COG5143
Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion];
3-155 5.14e-18

Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion];


Pssm-ID: 227472 [Multi-domain]  Cd Length: 190  Bit Score: 76.70  E-value: 5.14e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393428100   3 LYSLSVLYKGEAKVVLLKAAYDVSSFSFFQRSSVQEFMTFTSQliversSKGTRASVKEQDYLCHVYVRNDSLAGVVIAD 82
Cdd:COG5143     1 IASISLFRVKGEPLRTLSDAESLSSFSFFHRSKVKEVLRFLSK------TSASRASIESGDYFFHYLKMSSGIVYVPISD 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1393428100  83 NEYPSRVAFTLLEKVLDEFSKQVDRIDWpVGSPATIHYPALDGHLSR-YQNPREADPMTKVQAELDETKIILAR 155
Cdd:COG5143    75 KEYPNKLAYGYLNSIATEFLKSSALEQL-IDDTVGIMRVNIDKVIEKgYRDPSIQDKLDQLQQELEETKRVLNK 147
R-SNARE_YKT6 cd15867
SNARE motif of YKT6; Ykt6 forms complexes with syntaxin-5 (Qa), GS28 (Qb) and either Bet1 (Qc) ...
 136-153 1.64e-06

SNARE motif of YKT6; Ykt6 forms complexes with syntaxin-5 (Qa), GS28 (Qb) and either Bet1 (Qc) or GS15 (Qc). This complex regulates the early secretory pathway of eukaryotic cells at the level of the transport from the ER-Golgi intermediate compartment (ERGIC) to the cis-Golgi and transport from the trans-Golgi network to the cis-Golgi, respectively. Ykt6 is a member of the R-SNARE subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles.


Pssm-ID: 277220  Cd Length: 61  Bit Score: 43.13  E-value: 1.64e-06
                          10
                  ....*....|....*...
gi 1393428100 136 ADPMTKVQAELDETKIIL 153
Cdd:cd15867     1 ADKIMKVQSELDETKIIL 18
 
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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