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Conserved domains on  [gi|493457489|ref|WP_006412743|]
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type VI secretion system contractile sheath small subunit [Burkholderia multivorans]

Protein Classification

type VI secretion system contractile sheath small subunit( domain architecture ID 10007505)

type VI secretion system contractile sheath small subunit TssB/VipA assembles with the large subunit TssC/VipB to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TssB COG3516
Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, ...
 3-172 1.07e-88

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


:

Pssm-ID: 442738  Cd Length: 171  Bit Score: 257.03  E-value: 1.07e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489   3 ASSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGKhPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVA 82
Cdd:COG3516    2 SESKQKFLSRVRKPRVQITYDVETGGAEEKKELPFVMGVLGDLSGK-PEEPLPPLKERKFVEIDKDNFDDVMKAIAPRLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489  83 FAVPNTLTGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAA 161
Cdd:COG3516   81 FSVPNTLSGDGgELNVDLTFESMDDFSPEAVARQVPPLRKLLEAREALADLKGKLDGNPALEKLLEKVLQDPELLQALAA 160

                        170
                 ....*....|.
gi 493457489 162 APRPERHEADA 172
Cdd:COG3516  161 ELGAEAEAEED 171
 
Name Accession Description Interval E-value
TssB COG3516
Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, ...
 3-172 1.07e-88

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


Pssm-ID: 442738  Cd Length: 171  Bit Score: 257.03  E-value: 1.07e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489   3 ASSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGKhPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVA 82
Cdd:COG3516    2 SESKQKFLSRVRKPRVQITYDVETGGAEEKKELPFVMGVLGDLSGK-PEEPLPPLKERKFVEIDKDNFDDVMKAIAPRLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489  83 FAVPNTLTGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAA 161
Cdd:COG3516   81 FSVPNTLSGDGgELNVDLTFESMDDFSPEAVARQVPPLRKLLEAREALADLKGKLDGNPALEKLLEKVLQDPELLQALAA 160

                        170
                 ....*....|.
gi 493457489 162 APRPERHEADA 172
Cdd:COG3516  161 ELGAEAEAEED 171
T6SS_VipA pfam05591
Type VI secretion system, VipA, VC_A0107 or Hcp2; T6SSs are toxin delivery systems. It is a ...
 10-163 7.21e-77

Type VI secretion system, VipA, VC_A0107 or Hcp2; T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. VipA is a family of Gram-negative bacterial proteins that form part of the type VI pathogenic secretion system. Members have been variously defined as VC_A0107 family, Hcp2, TssB and VipA, for ClpV-interacting proteins. VipB and VipA proteins interact very closely to form the shaft of the pathogenic penetrating needle system. VipA and VipB (TssB and TssC) proteins were shown to form a cog-wheel like tubular structure in V. cholerae that was noticed to resemble T4 phage gp18 polysheath. Two beta-strands of VipA and four beta-strands of VipB intertwine forming the middle layer of the sheath. The sheath assembles around an inner Hcp tube and is attached to a structure called a baseplate that spans the bacterial membranes. Importantly, VipA/VipB sheath was shown to form a long contractile organelle in V. cholerae and in E. coli, suggesting that sheath contraction powers the secretion.


Pssm-ID: 428529  Cd Length: 154  Bit Score: 226.20  E-value: 7.21e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489   10 IARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGKhPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVAFAVPNTL 89
Cdd:pfam05591   1 LSRVPKPRVNITYDVETGGAQEKVELPFVMGVLGDFSGK-PTEPLPPLEDRKFVNIDKDNFDDVMKAMNPRLAFSVPNTL 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493457489   90 TGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAAAP 163
Cdd:pfam05591  80 SGDGsELAVDLKFESMKDFSPDAVARQVPELRKLLELREALADLKGPLDNNPALRKLLEEILSDPELLEKLLSEL 154
VI_chp_5 TIGR03358
type VI secretion protein, VC_A0107 family; Work by Mougous, et al. (2006), describes ...
 8-163 1.91e-72

type VI secretion protein, VC_A0107 family; Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]


Pssm-ID: 132401  Cd Length: 159  Bit Score: 215.22  E-value: 1.91e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489    8 KFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGkHPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVAFAVPN 87
Cdd:TIGR03358   1 KKLSRVRKPRVQITYDVETGGAEEKVELPLVVGVLGDLSG-GPTEPLTPLEERKFVEVDKDNFDEVMEAMNPRLSFAVKN 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493457489   88 TLTGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAAAP 163
Cdd:TIGR03358  80 TLSDDGeELPVDLKFESMDDFSPDAVAKQVPELKKLLEAREALRDLKGPLDNNPDLRKLLQELLKDKDLLEKLLSEL 156
PRK05329 PRK05329
glycerol-3-phosphate dehydrogenase subunit GlpB;
80-173 6.98e-03

glycerol-3-phosphate dehydrogenase subunit GlpB;


Pssm-ID: 235412  Cd Length: 422  Bit Score: 36.37  E-value: 6.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489  80 RVAFAVPNT-----LTGEGQMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTyMDGKSGAEALVT---QLLQ 151
Cdd:PRK05329 120 RPTWLSPPSvpagvALLDAKRILVVGIEGLRDFQPHLAAANLHAQFQGLEVRTAELELPG-LDRDNPREFRAVniaRLLD 198

                         90       100
                 ....*....|....*....|..
gi 493457489 152 DPALLKSLAAAPRPERHEADAA 173
Cdd:PRK05329 199 DPENREALADALKPLAGDAEAV 220
 
Name Accession Description Interval E-value
TssB COG3516
Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, ...
 3-172 1.07e-88

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


Pssm-ID: 442738  Cd Length: 171  Bit Score: 257.03  E-value: 1.07e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489   3 ASSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGKhPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVA 82
Cdd:COG3516    2 SESKQKFLSRVRKPRVQITYDVETGGAEEKKELPFVMGVLGDLSGK-PEEPLPPLKERKFVEIDKDNFDDVMKAIAPRLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489  83 FAVPNTLTGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAA 161
Cdd:COG3516   81 FSVPNTLSGDGgELNVDLTFESMDDFSPEAVARQVPPLRKLLEAREALADLKGKLDGNPALEKLLEKVLQDPELLQALAA 160

                        170
                 ....*....|.
gi 493457489 162 APRPERHEADA 172
Cdd:COG3516  161 ELGAEAEAEED 171
T6SS_VipA pfam05591
Type VI secretion system, VipA, VC_A0107 or Hcp2; T6SSs are toxin delivery systems. It is a ...
 10-163 7.21e-77

Type VI secretion system, VipA, VC_A0107 or Hcp2; T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. VipA is a family of Gram-negative bacterial proteins that form part of the type VI pathogenic secretion system. Members have been variously defined as VC_A0107 family, Hcp2, TssB and VipA, for ClpV-interacting proteins. VipB and VipA proteins interact very closely to form the shaft of the pathogenic penetrating needle system. VipA and VipB (TssB and TssC) proteins were shown to form a cog-wheel like tubular structure in V. cholerae that was noticed to resemble T4 phage gp18 polysheath. Two beta-strands of VipA and four beta-strands of VipB intertwine forming the middle layer of the sheath. The sheath assembles around an inner Hcp tube and is attached to a structure called a baseplate that spans the bacterial membranes. Importantly, VipA/VipB sheath was shown to form a long contractile organelle in V. cholerae and in E. coli, suggesting that sheath contraction powers the secretion.


Pssm-ID: 428529  Cd Length: 154  Bit Score: 226.20  E-value: 7.21e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489   10 IARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGKhPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVAFAVPNTL 89
Cdd:pfam05591   1 LSRVPKPRVNITYDVETGGAQEKVELPFVMGVLGDFSGK-PTEPLPPLEDRKFVNIDKDNFDDVMKAMNPRLAFSVPNTL 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493457489   90 TGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAAAP 163
Cdd:pfam05591  80 SGDGsELAVDLKFESMKDFSPDAVARQVPELRKLLELREALADLKGPLDNNPALRKLLEEILSDPELLEKLLSEL 154
VI_chp_5 TIGR03358
type VI secretion protein, VC_A0107 family; Work by Mougous, et al. (2006), describes ...
 8-163 1.91e-72

type VI secretion protein, VC_A0107 family; Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]


Pssm-ID: 132401  Cd Length: 159  Bit Score: 215.22  E-value: 1.91e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489    8 KFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGkHPVEPLPAVSERRFLEIDIDNFDERMKAIRPRVAFAVPN 87
Cdd:TIGR03358   1 KKLSRVRKPRVQITYDVETGGAEEKVELPLVVGVLGDLSG-GPTEPLTPLEERKFVEVDKDNFDEVMEAMNPRLSFAVKN 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493457489   88 TLTGEG-QMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTYMDGKSGAEALVTQLLQDPALLKSLAAAP 163
Cdd:TIGR03358  80 TLSDDGeELPVDLKFESMDDFSPDAVAKQVPELKKLLEAREALRDLKGPLDNNPDLRKLLQELLKDKDLLEKLLSEL 156
PRK05329 PRK05329
glycerol-3-phosphate dehydrogenase subunit GlpB;
80-173 6.98e-03

glycerol-3-phosphate dehydrogenase subunit GlpB;


Pssm-ID: 235412  Cd Length: 422  Bit Score: 36.37  E-value: 6.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493457489  80 RVAFAVPNT-----LTGEGQMMVDMTFESMEDFSPAAIADKVEPLRRLLQARTQLANLQTyMDGKSGAEALVT---QLLQ 151
Cdd:PRK05329 120 RPTWLSPPSvpagvALLDAKRILVVGIEGLRDFQPHLAAANLHAQFQGLEVRTAELELPG-LDRDNPREFRAVniaRLLD 198

                         90       100
                 ....*....|....*....|..
gi 493457489 152 DPALLKSLAAAPRPERHEADAA 173
Cdd:PRK05329 199 DPENREALADALKPLAGDAEAV 220
 
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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