NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15595281|ref|NP_248773|]
View 

hypothetical protein PA0083 [Pseudomonas aeruginosa PAO1]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TssB COG3516
Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, ...
 6-172 4.78e-89

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


:

Pssm-ID: 442738  Cd Length: 171  Bit Score: 257.42  E-value: 4.78e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281   6 SSQKFIARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNV 85
Cdd:COG3516   4 SKQKFLSRVRKPRVQITYDVETGGAEEKKELPFVMGVLGDLSGKPEEPLPPLKERKFVEIDKDNFDDVMKAIAPRLAFSV 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281  86 PNVLTGEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAPK 164
Cdd:COG3516  84 PNTLSGDGgELNVDLTFESMDDFSPEAVARQVPPLRKLLEAREALADLKGKLDGNPALEKLLEKVLQDPELLQALAAELG 163


                ....*...
gi 15595281 165 PKDDEPQA 172
Cdd:COG3516 164 AEAEAEED 171
 
Name Accession Description Interval E-value
TssB COG3516
Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, ...
 6-172 4.78e-89

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


Pssm-ID: 442738  Cd Length: 171  Bit Score: 257.42  E-value: 4.78e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281   6 SSQKFIARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNV 85
Cdd:COG3516   4 SKQKFLSRVRKPRVQITYDVETGGAEEKKELPFVMGVLGDLSGKPEEPLPPLKERKFVEIDKDNFDDVMKAIAPRLAFSV 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281  86 PNVLTGEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAPK 164
Cdd:COG3516  84 PNTLSGDGgELNVDLTFESMDDFSPEAVARQVPPLRKLLEAREALADLKGKLDGNPALEKLLEKVLQDPELLQALAAELG 163


                ....*...
gi 15595281 165 PKDDEPQA 172
Cdd:COG3516 164 AEAEAEED 171
T6SS_VipA pfam05591
Type VI secretion system, VipA, VC_A0107 or Hcp2; T6SSs are toxin delivery systems. It is a ...
 11-163 2.72e-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: 226.97  E-value: 2.72e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281    11 IARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNVPNVLT 90
Cdd:pfam05591   1 LSRVPKPRVNITYDVETGGAQEKVELPFVMGVLGDFSGKPTEPLPPLEDRKFVNIDKDNFDDVMKAMNPRLAFSVPNTLS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595281    91 GEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAP 163
Cdd:pfam05591  81 GDGsELAVDLKFESMKDFSPDAVARQVPELRKLLELREALADLKGPLDNNPALRKLLEEILSDPELLEKLLSEL 154
VI_chp_5 TIGR03358
type VI secretion protein, VC_A0107 family; Work by Mougous, et al. (2006), describes ...
 9-164 3.91e-70

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: 209.06  E-value: 3.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281     9 KFIARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNVPNV 88
Cdd:TIGR03358   1 KKLSRVRKPRVQITYDVETGGAEEKVELPLVVGVLGDLSGGPTEPLTPLEERKFVEVDKDNFDEVMEAMNPRLSFAVKNT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15595281    89 LTGEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAPK 164
Cdd:TIGR03358  81 LSDDGeELPVDLKFESMDDFSPDAVAKQVPELKKLLEAREALRDLKGPLDNNPDLRKLLQELLKDKDLLEKLLSELG 157
 
Name Accession Description Interval E-value
TssB COG3516
Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, ...
 6-172 4.78e-89

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


Pssm-ID: 442738  Cd Length: 171  Bit Score: 257.42  E-value: 4.78e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281   6 SSQKFIARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNV 85
Cdd:COG3516   4 SKQKFLSRVRKPRVQITYDVETGGAEEKKELPFVMGVLGDLSGKPEEPLPPLKERKFVEIDKDNFDDVMKAIAPRLAFSV 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281  86 PNVLTGEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAPK 164
Cdd:COG3516  84 PNTLSGDGgELNVDLTFESMDDFSPEAVARQVPPLRKLLEAREALADLKGKLDGNPALEKLLEKVLQDPELLQALAAELG 163


                ....*...
gi 15595281 165 PKDDEPQA 172
Cdd:COG3516 164 AEAEAEED 171
T6SS_VipA pfam05591
Type VI secretion system, VipA, VC_A0107 or Hcp2; T6SSs are toxin delivery systems. It is a ...
 11-163 2.72e-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: 226.97  E-value: 2.72e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281    11 IARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNVPNVLT 90
Cdd:pfam05591   1 LSRVPKPRVNITYDVETGGAQEKVELPFVMGVLGDFSGKPTEPLPPLEDRKFVNIDKDNFDDVMKAMNPRLAFSVPNTLS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595281    91 GEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAP 163
Cdd:pfam05591  81 GDGsELAVDLKFESMKDFSPDAVARQVPELRKLLELREALADLKGPLDNNPALRKLLEEILSDPELLEKLLSEL 154
VI_chp_5 TIGR03358
type VI secretion protein, VC_A0107 family; Work by Mougous, et al. (2006), describes ...
 9-164 3.91e-70

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: 209.06  E-value: 3.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595281     9 KFIARNRAPRVQIEYDVELYGAEKKVQLPFVMGVMADLAGKPAEPQAAVADRKFLEIDVDNFDARLKAMKPRVAFNVPNV 88
Cdd:TIGR03358   1 KKLSRVRKPRVQITYDVETGGAEEKVELPLVVGVLGDLSGGPTEPLTPLEERKFVEVDKDNFDEVMEAMNPRLSFAVKNT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15595281    89 LTGEG-NLSLDITFESMDDFSPAAVARKVDSLNKLLEARTQLANLLTYMDGKTGAEEMIMKAIKDPALLQALASAPK 164
Cdd:TIGR03358  81 LSDDGeELPVDLKFESMDDFSPDAVAKQVPELKKLLEAREALRDLKGPLDNNPDLRKLLQELLKDKDLLEKLLSELG 157
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH