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Conserved domains on  [gi|589911157|pdb|4NHF|A]
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Chain A, TrwG protein

Protein Classification

type IV secretion system protein( domain architecture ID 11611546)

type IV secretion system (T4SS) protein functions as a virulence factor that plays important roles in mediating intracellular survival and manipulating host immune response to infection

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VirB8_like cd16384
virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar ...
 42-174 2.04e-68

virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar proteins which consist of cytoplasmic, transmembrane, and periplasmic regions. VirB8 is an essential assembly factor of type IV secretion system (T4SS) channel proteins that are highly diverse in function relative to other bacterial secretion systems. T4SS proteins are important virulence factors for many Gram-negative pathogens, such as Agrobacterium, Brucella, Legionella, and Helicobacter. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the nuclear transport factor-2 (NTF2) protein.


:

Pssm-ID: 319760  Cd Length: 133  Bit Score: 204.49  E-value: 2.04e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       42 EVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVR 121
Cdd:cd16384   1 EVVHASVLAFYVDLRETYDIDTIQRAYDMLSNNSATAVAQEYFNSSEASNPRDFKLAETQRVNVEIISVIPQSPGTWQVR 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
4NHF_A      122 FTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDP 174
Cdd:cd16384  81 WLEKVYDRQGHLTEPPFKMRATLRYYNVPTTQSEEQRLNNPLGIYITSYSWSK 133
 
Name Accession Description Interval E-value
VirB8_like cd16384
virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar ...
 42-174 2.04e-68

virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar proteins which consist of cytoplasmic, transmembrane, and periplasmic regions. VirB8 is an essential assembly factor of type IV secretion system (T4SS) channel proteins that are highly diverse in function relative to other bacterial secretion systems. T4SS proteins are important virulence factors for many Gram-negative pathogens, such as Agrobacterium, Brucella, Legionella, and Helicobacter. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the nuclear transport factor-2 (NTF2) protein.


Pssm-ID: 319760  Cd Length: 133  Bit Score: 204.49  E-value: 2.04e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       42 EVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVR 121
Cdd:cd16384   1 EVVHASVLAFYVDLRETYDIDTIQRAYDMLSNNSATAVAQEYFNSSEASNPRDFKLAETQRVNVEIISVIPQSPGTWQVR 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
4NHF_A      122 FTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDP 174
Cdd:cd16384  81 WLEKVYDRQGHLTEPPFKMRATLRYYNVPTTQSEEQRLNNPLGIYITSYSWSK 133
VirB8 COG3736
Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and ...
 13-179 1.08e-65

Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442950  Cd Length: 230  Bit Score: 200.99  E-value: 1.08e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       13 PTPLVLRVDNTTGAVDVISVMREHETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIY--DGE 90
Cdd:COG3736  63 VEPYVVRVDKSTGAVTVVTPLTEKQLTYNEAVDRYFLARYVRARESYDPATLQEDYDTVALLSSPDVQREYRALFssTNP 142

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       91 NARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTgPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSY 170
Cdd:COG3736 143 QSPDNVYGKGARRRVKILSISFLNDNTAQVRFTRTERDDTGGGT-QTTHWIATITFRYVNAPLSEEDRLINPLGFQVTSY 221


                ....*....
4NHF_A      171 RSDPEILLN 179
Cdd:COG3736 222 RVDPEYLPN 230
VirB8 pfam04335
VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and ...
 13-174 2.49e-40

VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the NTF2 protein.


Pssm-ID: 427873  Cd Length: 211  Bit Score: 135.55  E-value: 2.49e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A         13 PTPLVLRVDNTTGAVDVISVMREHETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDG--E 90
Cdd:pfam04335  47 VEPYVVEVDKTTGEVDAVAPATEKKPSADEAVIKAFLARYVTAREVYDDPILQDNYLRVYLFSTDSAADQLNDYFNSnnP 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A         91 NARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKqHQIATIGYTYVG--APMKSSDRLLNPLGFQIT 168
Cdd:pfam04335 127 NSPFALYGKEARVEVEIKSVIRISPNTAQVRFSETTRNRNGSLAYTT-RWTATLTFRYTVkdTPMTEEDRLINPLGFYVT 205


                  ....*.
4NHF_A        169 SYRSDP 174
Cdd:pfam04335 206 SYSWDK 211
PRK13865 PRK13865
type IV secretion system protein VirB8; Provisional
 13-172 2.01e-11

type IV secretion system protein VirB8; Provisional


Pssm-ID: 172386  Cd Length: 229  Bit Score: 60.31  E-value: 2.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A        13 PTPLVLRVDNTTGAVdvISVMREHETSYGEVVdRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENA 92
Cdd:PRK13865  69 PVYLWVRPDGTVDSE--VSVSRLPATQEQAVV-NASLWEYVRLRESYDADTAQYAYDLVSNFSAPTVRQDYQQFFNYPNP 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A        93 RDK--VLSNKARITVKVRSIQLNGLGQATVRFT-TQQLDSSGATTGPkqhQIATIGYTYVgAPMKSSDRLLNPLGFQITS 169
Cdd:PRK13865 146 TSPqvIVGKRGRLEVEHISSNDVTPGVQQIRYKrTLTMDGKMPVVST---WTATVRYEKV-TSLPGRLRLTNPGGLIVTS 221


                 ...
4NHF_A       170 YRS 172
Cdd:PRK13865 222 YQT 224
 
Name Accession Description Interval E-value
VirB8_like cd16384
virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar ...
 42-174 2.04e-68

virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar proteins which consist of cytoplasmic, transmembrane, and periplasmic regions. VirB8 is an essential assembly factor of type IV secretion system (T4SS) channel proteins that are highly diverse in function relative to other bacterial secretion systems. T4SS proteins are important virulence factors for many Gram-negative pathogens, such as Agrobacterium, Brucella, Legionella, and Helicobacter. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the nuclear transport factor-2 (NTF2) protein.


Pssm-ID: 319760  Cd Length: 133  Bit Score: 204.49  E-value: 2.04e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       42 EVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVR 121
Cdd:cd16384   1 EVVHASVLAFYVDLRETYDIDTIQRAYDMLSNNSATAVAQEYFNSSEASNPRDFKLAETQRVNVEIISVIPQSPGTWQVR 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
4NHF_A      122 FTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDP 174
Cdd:cd16384  81 WLEKVYDRQGHLTEPPFKMRATLRYYNVPTTQSEEQRLNNPLGIYITSYSWSK 133
VirB8 COG3736
Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and ...
 13-179 1.08e-65

Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442950  Cd Length: 230  Bit Score: 200.99  E-value: 1.08e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       13 PTPLVLRVDNTTGAVDVISVMREHETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIY--DGE 90
Cdd:COG3736  63 VEPYVVRVDKSTGAVTVVTPLTEKQLTYNEAVDRYFLARYVRARESYDPATLQEDYDTVALLSSPDVQREYRALFssTNP 142

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       91 NARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTgPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSY 170
Cdd:COG3736 143 QSPDNVYGKGARRRVKILSISFLNDNTAQVRFTRTERDDTGGGT-QTTHWIATITFRYVNAPLSEEDRLINPLGFQVTSY 221


                ....*....
4NHF_A      171 RSDPEILLN 179
Cdd:COG3736 222 RVDPEYLPN 230
VirB8 cd16424
periplasmic domain of VirB8 protein; This family contains the periplasmic domain of VirB8 ...
 39-174 4.13e-53

periplasmic domain of VirB8 protein; This family contains the periplasmic domain of VirB8 protein which is an essential assembly factor of type IV secretion system (T4SS) channel proteins that are highly diverse in function relative to other bacterial secretion systems. T4SS proteins are important virulence factors for many Gram-negative pathogens, such as Agrobacterium, Brucella, Legionella, and Helicobacter. VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that VirB8 is a primary constituent of a DNA transporter. It is a crucial structural and functional component of the T4SS, with interactions between VirB8 and many other T4SS proteins, including VirB10, VirB9, VirB1, VirB4, and VirB11, as well as with itself.


Pssm-ID: 319761  Cd Length: 137  Bit Score: 165.54  E-value: 4.13e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       39 SYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARD-KVLSNKARITVKVRSIQ-LNGLG 116
Cdd:cd16424   1 TYDEALDKYFLAQYVRARESYDWATLQEDYDTVRLMSSPDVAAEYRALFNGDNPPSpKVLGKNARVEVKILSISfLGGDN 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
4NHF_A      117 QATVRFTTQQLDSSGATTgPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDP 174
Cdd:cd16424  81 TAQVRFTKTIRDKGGGEP-TPTYWIATITFDYVPAPMTEEDRLINPLGFQVTSYRVDP 137
VirB8 pfam04335
VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and ...
 13-174 2.49e-40

VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the NTF2 protein.


Pssm-ID: 427873  Cd Length: 211  Bit Score: 135.55  E-value: 2.49e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A         13 PTPLVLRVDNTTGAVDVISVMREHETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDG--E 90
Cdd:pfam04335  47 VEPYVVEVDKTTGEVDAVAPATEKKPSADEAVIKAFLARYVTAREVYDDPILQDNYLRVYLFSTDSAADQLNDYFNSnnP 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A         91 NARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKqHQIATIGYTYVG--APMKSSDRLLNPLGFQIT 168
Cdd:pfam04335 127 NSPFALYGKEARVEVEIKSVIRISPNTAQVRFSETTRNRNGSLAYTT-RWTATLTFRYTVkdTPMTEEDRLINPLGFYVT 205


                  ....*.
4NHF_A        169 SYRSDP 174
Cdd:pfam04335 206 SYSWDK 211
PRK13865 PRK13865
type IV secretion system protein VirB8; Provisional
 13-172 2.01e-11

type IV secretion system protein VirB8; Provisional


Pssm-ID: 172386  Cd Length: 229  Bit Score: 60.31  E-value: 2.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A        13 PTPLVLRVDNTTGAVdvISVMREHETSYGEVVdRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENA 92
Cdd:PRK13865  69 PVYLWVRPDGTVDSE--VSVSRLPATQEQAVV-NASLWEYVRLRESYDADTAQYAYDLVSNFSAPTVRQDYQQFFNYPNP 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A        93 RDK--VLSNKARITVKVRSIQLNGLGQATVRFT-TQQLDSSGATTGPkqhQIATIGYTYVgAPMKSSDRLLNPLGFQITS 169
Cdd:PRK13865 146 TSPqvIVGKRGRLEVEHISSNDVTPGVQQIRYKrTLTMDGKMPVVST---WTATVRYEKV-TSLPGRLRLTNPGGLIVTS 221


                 ...
4NHF_A       170 YRS 172
Cdd:PRK13865 222 YQT 224
TrbF cd16425
conjugal transfer protein TrbF; This family includes the conjugal transfer protein family TrbF, ...
 46-170 1.34e-03

conjugal transfer protein TrbF; This family includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain is similar to the type IV secretion system (T4ASS) component VirB8 and possibly has a similar fold to the nuclear transport factor-2 (NTF-2)-like superfamily.


Pssm-ID: 319762  Cd Length: 133  Bit Score: 37.22  E-value: 1.34e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4NHF_A       46 RYWLNQYVLN-RENYDYDTIQLNY--DTTALLSAASVQQ--EYYKIYDGENARDKVLsnkarITVKVRSIQLNGLGQATV 120
Cdd:cd16425   7 RYFLADFIENvRTVSPDPVAQKKNikRAYAFLTGGAAAKlnEYYRENNPFERAGKET-----VSVEITSVLPLSDNTWQV 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
4NHF_A      121 RFTTQQLDSSGATTGPKqHQIATIGYTYVgAPMKSSDRLLNPLGFQITSY 170
Cdd:cd16425  82 EWTETTRDRGGGVISTE-RYRATFTVKIV-PPTTEEQLLKNPLGIYITDF 129
 
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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