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Conserved domains on  [gi|1100260284|gb|OIK41813|]
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type VI secretion protein [Citrobacter portucalensis]

Protein Classification

type VI secretion system baseplate subunit TssE( domain architecture ID 10022389)

type VI secretion system (T6SS) baseplate subunit TssE is a component of the T6SS baseplate that serves not only as the tail assembly platform, but also docks the tail to the membrane complex

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VI_zyme TIGR03357
type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 ...
 8-139 3.32e-40

type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.


:

Pssm-ID: 274540  Cd Length: 133  Bit Score: 131.19  E-value: 3.32e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284   8 GGSLFERIGEAAK--PSSRQRPKTALLHSIRDNLRNILNTRSGSCYGSPELGITDFIDRPPERQNIREWMVQAIQNCILR 85
Cdd:TIGR03357   1 TPSLFERLPDASGesPSTRRSSAEQLRESIRRHLERLLNTRRGSCASLPDYGLPDLNDLSLSSADDRRRIRRAIEQAIER 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1100260284  86 YEPRISDVAVTAAtEDSHAPLNLRFHIVAYMDFSDRQDVLEFDILLDNHQHWCV 139
Cdd:TIGR03357  81 YEPRLSRVRVTAL-PDEEDPLALRFRIEAELDVDGGPEPVSFDALLDPSGRYRV 133
 
Name Accession Description Interval E-value
VI_zyme TIGR03357
type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 ...
 8-139 3.32e-40

type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.


Pssm-ID: 274540  Cd Length: 133  Bit Score: 131.19  E-value: 3.32e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284   8 GGSLFERIGEAAK--PSSRQRPKTALLHSIRDNLRNILNTRSGSCYGSPELGITDFIDRPPERQNIREWMVQAIQNCILR 85
Cdd:TIGR03357   1 TPSLFERLPDASGesPSTRRSSAEQLRESIRRHLERLLNTRRGSCASLPDYGLPDLNDLSLSSADDRRRIRRAIEQAIER 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1100260284  86 YEPRISDVAVTAAtEDSHAPLNLRFHIVAYMDFSDRQDVLEFDILLDNHQHWCV 139
Cdd:TIGR03357  81 YEPRLSRVRVTAL-PDEEDPLALRFRIEAELDVDGGPEPVSFDALLDPSGRYRV 133
COG3518 COG3518
Predicted component of the type VI protein secretion system [Intracellular trafficking, ...
 4-140 1.23e-28

Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442740  Cd Length: 162  Bit Score: 102.75  E-value: 1.23e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284   4 ERESGGSLFERIGEAAK------PSSRQRPKTALLHSIRDNLRNILNTRSGSC----------YGSPELGITDFIDRPPE 67
Cdd:COG3518     7 RRRLQPSLLDRLTDDEPdrsresPLSRVVSLEQLRESVRRDLEWLLNTRRGEAsllaaypevrRSVLNYGLPDLSGASLG 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1100260284  68 RQNIREWMVQAIQNCILRYEPRISDVAVTAATEDSHAPLNLRFHIVAYMDFSDRQDVLEFDILLD-NHQHWCVE 140
Cdd:COG3518    87 SPDDREAIERAIRQAILRFEPRLRRVSVTVLPDDDDSPNTLRFRIEAVLWADPAPEPVRFDTVLDlETGRVSVS 160
GPW_gp25 pfam04965
Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like ...
 29-114 6.55e-15

Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerization, playing a critical role in sheath assembly and contraction. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologs from the RpoS-mediated general stress response system (called IraD). This motif interacts with the 'core bundle' composed of orthologs of T4 gp6 and gp7 proteins in contractile injection systems.


Pssm-ID: 428225  Cd Length: 93  Bit Score: 65.29  E-value: 6.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284  29 TALLHSIRDNLRNILNTRSGSCYGSPELGITDFIDR-PPERQNIREWMVQAIQNCILRYEPRISDVAVTAAtEDSHAPLN 107
Cdd:pfam04965   1 SSLRESVRRDLEILLNTRPGERVSRPNYGCPDLALLfAPNDDATRALIERAIREAILRFEPRIRVVSVEVD-PDPDSPGT 79


                  ....*..
gi 1100260284 108 LRFHIVA 114
Cdd:pfam04965  80 LRFTIEY 86
25 PHA00415
baseplate wedge subunit
 34-126 1.31e-03

baseplate wedge subunit


Pssm-ID: 222788  Cd Length: 131  Bit Score: 36.52  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284  34 SIRDNLRNILNTRSGSCYGSPELGiTDFIDRPPErqNIREWMVQA----IQNCILRYEPRIS--DVAVTAATEDSHAPLN 107
Cdd:PHA00415   32 AIKNSLLGIVTTRKGERPFDPNFG-CDISDQLFE--NMDPLTADTiernIESAIRNYEPRVYnlNVEVIPVYDDNSIIVT 108

                          90
                  ....*....|....*....
gi 1100260284 108 LRFHIVaymdfsDRQDVLE 126
Cdd:PHA00415  109 IYFSII------DNPDDLE 121
 
Name Accession Description Interval E-value
VI_zyme TIGR03357
type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 ...
 8-139 3.32e-40

type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.


Pssm-ID: 274540  Cd Length: 133  Bit Score: 131.19  E-value: 3.32e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284   8 GGSLFERIGEAAK--PSSRQRPKTALLHSIRDNLRNILNTRSGSCYGSPELGITDFIDRPPERQNIREWMVQAIQNCILR 85
Cdd:TIGR03357   1 TPSLFERLPDASGesPSTRRSSAEQLRESIRRHLERLLNTRRGSCASLPDYGLPDLNDLSLSSADDRRRIRRAIEQAIER 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1100260284  86 YEPRISDVAVTAAtEDSHAPLNLRFHIVAYMDFSDRQDVLEFDILLDNHQHWCV 139
Cdd:TIGR03357  81 YEPRLSRVRVTAL-PDEEDPLALRFRIEAELDVDGGPEPVSFDALLDPSGRYRV 133
COG3518 COG3518
Predicted component of the type VI protein secretion system [Intracellular trafficking, ...
 4-140 1.23e-28

Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442740  Cd Length: 162  Bit Score: 102.75  E-value: 1.23e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284   4 ERESGGSLFERIGEAAK------PSSRQRPKTALLHSIRDNLRNILNTRSGSC----------YGSPELGITDFIDRPPE 67
Cdd:COG3518     7 RRRLQPSLLDRLTDDEPdrsresPLSRVVSLEQLRESVRRDLEWLLNTRRGEAsllaaypevrRSVLNYGLPDLSGASLG 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1100260284  68 RQNIREWMVQAIQNCILRYEPRISDVAVTAATEDSHAPLNLRFHIVAYMDFSDRQDVLEFDILLD-NHQHWCVE 140
Cdd:COG3518    87 SPDDREAIERAIRQAILRFEPRLRRVSVTVLPDDDDSPNTLRFRIEAVLWADPAPEPVRFDTVLDlETGRVSVS 160
GPW_gp25 pfam04965
Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like ...
 29-114 6.55e-15

Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerization, playing a critical role in sheath assembly and contraction. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologs from the RpoS-mediated general stress response system (called IraD). This motif interacts with the 'core bundle' composed of orthologs of T4 gp6 and gp7 proteins in contractile injection systems.


Pssm-ID: 428225  Cd Length: 93  Bit Score: 65.29  E-value: 6.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284  29 TALLHSIRDNLRNILNTRSGSCYGSPELGITDFIDR-PPERQNIREWMVQAIQNCILRYEPRISDVAVTAAtEDSHAPLN 107
Cdd:pfam04965   1 SSLRESVRRDLEILLNTRPGERVSRPNYGCPDLALLfAPNDDATRALIERAIREAILRFEPRIRVVSVEVD-PDPDSPGT 79


                  ....*..
gi 1100260284 108 LRFHIVA 114
Cdd:pfam04965  80 LRFTIEY 86
COG3628 COG3628
Phage baseplate assembly protein W [Mobilome: prophages, transposons];
34-101 7.59e-08

Phage baseplate assembly protein W [Mobilome: prophages, transposons];


Pssm-ID: 442846  Cd Length: 119  Bit Score: 47.56  E-value: 7.59e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1100260284  34 SIRDNLRNILNTRSGSC-----YGSpelGITDFIDRPPERQNIREwMVQAIQNCILRYEPRIS--DVAVTAATED 101
Cdd:COG3628    21 HIRQSIRIILTTPPGERvmrpdFGS---GLHDLLFEPNNPATALL-IRAAVAEALLRWEPRIEveSVDVTPDPEE 91
25 PHA00415
baseplate wedge subunit
 34-126 1.31e-03

baseplate wedge subunit


Pssm-ID: 222788  Cd Length: 131  Bit Score: 36.52  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1100260284  34 SIRDNLRNILNTRSGSCYGSPELGiTDFIDRPPErqNIREWMVQA----IQNCILRYEPRIS--DVAVTAATEDSHAPLN 107
Cdd:PHA00415   32 AIKNSLLGIVTTRKGERPFDPNFG-CDISDQLFE--NMDPLTADTiernIESAIRNYEPRVYnlNVEVIPVYDDNSIIVT 108

                          90
                  ....*....|....*....
gi 1100260284 108 LRFHIVaymdfsDRQDVLE 126
Cdd:PHA00415  109 IYFSII------DNPDDLE 121
 
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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