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Conserved domains on  [gi|1225319181|ref|WP_093329967|]
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SecY-interacting protein [Thalassotalea agarivorans]

Protein Classification

SecY-interacting protein Syd( domain architecture ID 11611341)

SecY-interacting protein Syd binds preferentially to an uncomplexed state of SecY, functioning either as a chelating agent for excess SecY in the cell or as a regulatory factor that negatively controls the translocase function

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Syd cd16323
Syd, a SecY-interacting protein; This family contains the Syd protein that has been implicated ...
 7-179 4.69e-87

Syd, a SecY-interacting protein; This family contains the Syd protein that has been implicated in the Sec-dependent transport of polypeptides across the inner membrane in bacteria. Syd has been shown to bind the SecY subunit of membrane-embedded SecYEG heterotrimer (also known as core translocon or SecY complex) which is a conserved protein-conducting channel essential for the biogenesis of most of the secretory and integral membrane proteins. The SecY-binding site of Syd is a conserved concave and electronegative groove that forms interactions with the electropositive loops of the SecY subunit. Syd is also known to verify the proper assembly of the SecY complex in the membrane by interfering with protein translocation only when the channel displays abnormal SecY-SecE associations. Operon analysis has shown that Syd protein may function as immunity protein in bacterial toxin systems.


:

Pssm-ID: 319993  Cd Length: 173  Bit Score: 253.21  E-value: 4.69e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   7 KNAVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYCFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSV 86
Cdd:cd16323     1 KQALEQFFERYIQAWQEQLGSLPKTEYDEEWPSPCEGEEDEEGYVYWQPVEREPPADFSNLEQALEITLHPDIKAFYGSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  87 YSEDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHK 166
Cdd:cd16323    81 YAGDLPATFQGGELELLQVWNEDDFERLQQNLIGHLLMKRRLKQPPTLFIGLTDDDDLLISVDNETGEVWLEDVGKEPHE 160

                         170
                  ....*....|...
gi 1225319181 167 KIADSLAEFMAQL 179
Cdd:cd16323   161 VLADSLAEFLSQL 173
 
Name Accession Description Interval E-value
Syd cd16323
Syd, a SecY-interacting protein; This family contains the Syd protein that has been implicated ...
 7-179 4.69e-87

Syd, a SecY-interacting protein; This family contains the Syd protein that has been implicated in the Sec-dependent transport of polypeptides across the inner membrane in bacteria. Syd has been shown to bind the SecY subunit of membrane-embedded SecYEG heterotrimer (also known as core translocon or SecY complex) which is a conserved protein-conducting channel essential for the biogenesis of most of the secretory and integral membrane proteins. The SecY-binding site of Syd is a conserved concave and electronegative groove that forms interactions with the electropositive loops of the SecY subunit. Syd is also known to verify the proper assembly of the SecY complex in the membrane by interfering with protein translocation only when the channel displays abnormal SecY-SecE associations. Operon analysis has shown that Syd protein may function as immunity protein in bacterial toxin systems.


Pssm-ID: 319993  Cd Length: 173  Bit Score: 253.21  E-value: 4.69e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   7 KNAVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYCFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSV 86
Cdd:cd16323     1 KQALEQFFERYIQAWQEQLGSLPKTEYDEEWPSPCEGEEDEEGYVYWQPVEREPPADFSNLEQALEITLHPDIKAFYGSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  87 YSEDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHK 166
Cdd:cd16323    81 YAGDLPATFQGGELELLQVWNEDDFERLQQNLIGHLLMKRRLKQPPTLFIGLTDDDDLLISVDNETGEVWLEDVGKEPHE 160

                         170
                  ....*....|...
gi 1225319181 167 KIADSLAEFMAQL 179
Cdd:cd16323   161 VLADSLAEFLSQL 173
Syd pfam07348
Syd protein (SUKH-2); This family contains a number of bacterial Syd proteins approximately ...
 9-181 2.79e-81

Syd protein (SUKH-2); This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association. Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems.


Pssm-ID: 429420  Cd Length: 174  Bit Score: 238.65  E-value: 2.79e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   9 AVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYCFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSVYS 88
Cdd:pfam07348   2 ALSAFTQRYVQLWQQETGELPRSEYLEGWPSPCILGTGDEGAVYWQPVPREEPADFDNVEKALEITLHPDIHAFYGSQYS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  89 EDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHKKI 168
Cdd:pfam07348  82 GDLPASFEGGELELLQVWSEDDFERLQENLIGHLLMQRRLKQPPTLFIATTDDEDRLVSVCNLSGEVWLEQLGKKPREVL 161

                         170
                  ....*....|...
gi 1225319181 169 ADSLAEFMAQLTP 181
Cdd:pfam07348 162 ADSLAEFLQQLEP 174
PRK04968 PRK04968
SecY interacting protein Syd; Provisional
 9-183 5.00e-80

SecY interacting protein Syd; Provisional


Pssm-ID: 235324  Cd Length: 181  Bit Score: 235.55  E-value: 5.00e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   9 AVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYcFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSVYS 88
Cdd:PRK04968    6 ALDDFTQRYCDAWQEEHGELPRSEELYGVPSPCIIETSEDAV-YWQPQPFEPEGNFNNVERALEITLHPDIHAFYTTQFA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  89 EDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHKKI 168
Cdd:PRK04968   85 GDMTAQFGGGELTLLQVWSEDDFERLQENLIGHLVMQKRLKLPPTLFIATTDEEDEVISVCNLSGEVILETLGTRKRTVL 164

                         170
                  ....*....|....*
gi 1225319181 169 ADSLAEFMAQLTPYV 183
Cdd:PRK04968  165 APSLAEFLNQLEPLL 179
SMI1_KNR4 smart00860
SMI1 / KNR4 family; Proteins in this family are involved in the regulation of 1,3-beta-glucan ...
 59-176 3.18e-03

SMI1 / KNR4 family; Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation.


Pssm-ID: 214864  Cd Length: 127  Bit Score: 36.08  E-value: 3.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   59 ADDINFDNVEQALELSFHQDIKDyFLSVYSEDIHASHSEGRLSLLFAWNQDDFDRLQ--QNIIGHILMKRKLKQAETVFF 136
Cdd:smart00860   2 ATEEEIAELEKKLGIKLPEDYKE-FLLLYNGGELGGSAELPLGGLSLLDLLELEAAIedQEEIDSDIEEEEYALPGWLIF 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1225319181  137 AVTDQEDMILSVLNSTGEVWVEQVGKEPH-------KKIADSLAEFM 176
Cdd:smart00860  81 IADGGGGGILIDLDDGPGGEGGEVGVILFgddddekYVVADSFEEFL 127
 
Name Accession Description Interval E-value
Syd cd16323
Syd, a SecY-interacting protein; This family contains the Syd protein that has been implicated ...
 7-179 4.69e-87

Syd, a SecY-interacting protein; This family contains the Syd protein that has been implicated in the Sec-dependent transport of polypeptides across the inner membrane in bacteria. Syd has been shown to bind the SecY subunit of membrane-embedded SecYEG heterotrimer (also known as core translocon or SecY complex) which is a conserved protein-conducting channel essential for the biogenesis of most of the secretory and integral membrane proteins. The SecY-binding site of Syd is a conserved concave and electronegative groove that forms interactions with the electropositive loops of the SecY subunit. Syd is also known to verify the proper assembly of the SecY complex in the membrane by interfering with protein translocation only when the channel displays abnormal SecY-SecE associations. Operon analysis has shown that Syd protein may function as immunity protein in bacterial toxin systems.


Pssm-ID: 319993  Cd Length: 173  Bit Score: 253.21  E-value: 4.69e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   7 KNAVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYCFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSV 86
Cdd:cd16323     1 KQALEQFFERYIQAWQEQLGSLPKTEYDEEWPSPCEGEEDEEGYVYWQPVEREPPADFSNLEQALEITLHPDIKAFYGSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  87 YSEDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHK 166
Cdd:cd16323    81 YAGDLPATFQGGELELLQVWNEDDFERLQQNLIGHLLMKRRLKQPPTLFIGLTDDDDLLISVDNETGEVWLEDVGKEPHE 160

                         170
                  ....*....|...
gi 1225319181 167 KIADSLAEFMAQL 179
Cdd:cd16323   161 VLADSLAEFLSQL 173
Syd pfam07348
Syd protein (SUKH-2); This family contains a number of bacterial Syd proteins approximately ...
 9-181 2.79e-81

Syd protein (SUKH-2); This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association. Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems.


Pssm-ID: 429420  Cd Length: 174  Bit Score: 238.65  E-value: 2.79e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   9 AVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYCFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSVYS 88
Cdd:pfam07348   2 ALSAFTQRYVQLWQQETGELPRSEYLEGWPSPCILGTGDEGAVYWQPVPREEPADFDNVEKALEITLHPDIHAFYGSQYS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  89 EDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHKKI 168
Cdd:pfam07348  82 GDLPASFEGGELELLQVWSEDDFERLQENLIGHLLMQRRLKQPPTLFIATTDDEDRLVSVCNLSGEVWLEQLGKKPREVL 161

                         170
                  ....*....|...
gi 1225319181 169 ADSLAEFMAQLTP 181
Cdd:pfam07348 162 ADSLAEFLQQLEP 174
PRK04968 PRK04968
SecY interacting protein Syd; Provisional
 9-183 5.00e-80

SecY interacting protein Syd; Provisional


Pssm-ID: 235324  Cd Length: 181  Bit Score: 235.55  E-value: 5.00e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   9 AVVQFTQQYTEQFEQAHGHLPVAEKDAQWPSPCEAGDKDNEYcFWTPKPIADDINFDNVEQALELSFHQDIKDYFLSVYS 88
Cdd:PRK04968    6 ALDDFTQRYCDAWQEEHGELPRSEELYGVPSPCIIETSEDAV-YWQPQPFEPEGNFNNVERALEITLHPDIHAFYTTQFA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181  89 EDIHASHSEGRLSLLFAWNQDDFDRLQQNIIGHILMKRKLKQAETVFFAVTDQEDMILSVLNSTGEVWVEQVGKEPHKKI 168
Cdd:PRK04968   85 GDMTAQFGGGELTLLQVWSEDDFERLQENLIGHLVMQKRLKLPPTLFIATTDEEDEVISVCNLSGEVILETLGTRKRTVL 164

                         170
                  ....*....|....*
gi 1225319181 169 ADSLAEFMAQLTPYV 183
Cdd:PRK04968  165 APSLAEFLNQLEPLL 179
SMI1_KNR4 smart00860
SMI1 / KNR4 family; Proteins in this family are involved in the regulation of 1,3-beta-glucan ...
 59-176 3.18e-03

SMI1 / KNR4 family; Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation.


Pssm-ID: 214864  Cd Length: 127  Bit Score: 36.08  E-value: 3.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1225319181   59 ADDINFDNVEQALELSFHQDIKDyFLSVYSEDIHASHSEGRLSLLFAWNQDDFDRLQ--QNIIGHILMKRKLKQAETVFF 136
Cdd:smart00860   2 ATEEEIAELEKKLGIKLPEDYKE-FLLLYNGGELGGSAELPLGGLSLLDLLELEAAIedQEEIDSDIEEEEYALPGWLIF 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1225319181  137 AVTDQEDMILSVLNSTGEVWVEQVGKEPH-------KKIADSLAEFM 176
Cdd:smart00860  81 IADGGGGGILIDLDDGPGGEGGEVGVILFgddddekYVVADSFEEFL 127
 
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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