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Conserved domains on  [gi|90109096|pdb|2CC3|A]
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Chain A, PROTEIN VIRB8

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VirB8 super family cl01500
VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and ...
 5-142 1.59e-97

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.


The actual alignment was detected with superfamily member PRK13865:

Pssm-ID: 445436  Cd Length: 229  Bit Score: 280.26  E-value: 1.59e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A         5 TQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPG 84
Cdd:PRK13865  92 TQEQAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPTVRQDYQQFFNYPNPTSPQVIVGKRGRLEVEHISSNDVTPG 171

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
2CC3_A        85 VQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTV 142
Cdd:PRK13865 172 VQQIRYKRTLTMDGKMPVVSTWTATVRYEKVTSLPGRLRLTNPGGLIVTSYQTSEDTV 229
 
Name Accession Description Interval E-value
PRK13865 PRK13865
type IV secretion system protein VirB8; Provisional
 5-142 1.59e-97

type IV secretion system protein VirB8; Provisional


Pssm-ID: 172386  Cd Length: 229  Bit Score: 280.26  E-value: 1.59e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A         5 TQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPG 84
Cdd:PRK13865  92 TQEQAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPTVRQDYQQFFNYPNPTSPQVIVGKRGRLEVEHISSNDVTPG 171

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
2CC3_A        85 VQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTV 142
Cdd:PRK13865 172 VQQIRYKRTLTMDGKMPVVSTWTATVRYEKVTSLPGRLRLTNPGGLIVTSYQTSEDTV 229
VirB8_like cd16384
virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar ...
 8-139 1.46e-63

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: 190.62  E-value: 1.46e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A        8 EAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTspQVILGKHGRLEVEHIASNDVTPGVQQ 87
Cdd:cd16384   1 EVVHASVLAFYVDLRETYDIDTIQRAYDMLSNNSATAVAQEYFNSSEASNPR--DFKLAETQRVNVEIISVIPQSPGTWQ 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
2CC3_A       88 IRYKRTLIVDG--KMPMASTWTATVRYEKVTSLP-GRLRLTNPGGLVVTSYQTSE 139
Cdd:cd16384  79 VRWLEKVYDRQghLTEPPFKMRATLRYYNVPTTQsEEQRLNNPLGIYITSYSWSK 133
VirB8 COG3736
Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and ...
 3-144 1.81e-44

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


Pssm-ID: 442950  Cd Length: 230  Bit Score: 145.52  E-value: 1.81e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A        3 HMTQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVT 82
Cdd:COG3736  87 QLTYNEAVDRYFLARYVRARESYDPATLQEDYDTVALLSSPDVQREYRALFSSTNPQSPDNVYGKGARRRVKILSISFLN 166

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
2CC3_A       83 PGVQQIRYKRTLIVD-GKMPMASTWTATVRYEKV-TSLPGRLRLTNPGGLVVTSYQTSEDTVSN 144
Cdd:COG3736 167 DNTAQVRFTRTERDDtGGGTQTTHWIATITFRYVnAPLSEEDRLINPLGFQVTSYRVDPEYLPN 230
VirB8 pfam04335
VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and ...
 2-139 1.75e-41

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: 137.47  E-value: 1.75e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A          2 PHMTQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDV 81
Cdd:pfam04335  70 KKPSADEAVIKAFLARYVTAREVYDDPILQDNYLRVYLFSTDSAADQLNDYFNSNNPNSPFALYGKEARVEVEIKSVIRI 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
2CC3_A         82 TPGVQQIRYKRTLI-VDGKMPMASTWTATVRYE---KVTSLPGRLRLTNPGGLVVTSYQTSE 139
Cdd:pfam04335 150 SPNTAQVRFSETTRnRNGSLAYTTRWTATLTFRytvKDTPMTEEDRLINPLGFYVTSYSWDK 211
 
Name Accession Description Interval E-value
PRK13865 PRK13865
type IV secretion system protein VirB8; Provisional
 5-142 1.59e-97

type IV secretion system protein VirB8; Provisional


Pssm-ID: 172386  Cd Length: 229  Bit Score: 280.26  E-value: 1.59e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A         5 TQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPG 84
Cdd:PRK13865  92 TQEQAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPTVRQDYQQFFNYPNPTSPQVIVGKRGRLEVEHISSNDVTPG 171

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
2CC3_A        85 VQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTV 142
Cdd:PRK13865 172 VQQIRYKRTLTMDGKMPVVSTWTATVRYEKVTSLPGRLRLTNPGGLIVTSYQTSEDTV 229
VirB8_like cd16384
virulence protein VirB8; This family contains bacterial virulence protein VirB8 and similar ...
 8-139 1.46e-63

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: 190.62  E-value: 1.46e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A        8 EAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTspQVILGKHGRLEVEHIASNDVTPGVQQ 87
Cdd:cd16384   1 EVVHASVLAFYVDLRETYDIDTIQRAYDMLSNNSATAVAQEYFNSSEASNPR--DFKLAETQRVNVEIISVIPQSPGTWQ 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
2CC3_A       88 IRYKRTLIVDG--KMPMASTWTATVRYEKVTSLP-GRLRLTNPGGLVVTSYQTSE 139
Cdd:cd16384  79 VRWLEKVYDRQghLTEPPFKMRATLRYYNVPTTQsEEQRLNNPLGIYITSYSWSK 133
VirB8 COG3736
Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and ...
 3-144 1.81e-44

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


Pssm-ID: 442950  Cd Length: 230  Bit Score: 145.52  E-value: 1.81e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A        3 HMTQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVT 82
Cdd:COG3736  87 QLTYNEAVDRYFLARYVRARESYDPATLQEDYDTVALLSSPDVQREYRALFSSTNPQSPDNVYGKGARRRVKILSISFLN 166

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
2CC3_A       83 PGVQQIRYKRTLIVD-GKMPMASTWTATVRYEKV-TSLPGRLRLTNPGGLVVTSYQTSEDTVSN 144
Cdd:COG3736 167 DNTAQVRFTRTERDDtGGGTQTTHWIATITFRYVnAPLSEEDRLINPLGFQVTSYRVDPEYLPN 230
VirB8 pfam04335
VirB8 protein; VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and ...
 2-139 1.75e-41

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: 137.47  E-value: 1.75e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A          2 PHMTQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDV 81
Cdd:pfam04335  70 KKPSADEAVIKAFLARYVTAREVYDDPILQDNYLRVYLFSTDSAADQLNDYFNSNNPNSPFALYGKEARVEVEIKSVIRI 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
2CC3_A         82 TPGVQQIRYKRTLI-VDGKMPMASTWTATVRYE---KVTSLPGRLRLTNPGGLVVTSYQTSE 139
Cdd:pfam04335 150 SPNTAQVRFSETTRnRNGSLAYTTRWTATLTFRytvKDTPMTEEDRLINPLGFYVTSYSWDK 211
VirB8 cd16424
periplasmic domain of VirB8 protein; This family contains the periplasmic domain of VirB8 ...
 5-139 2.20e-35

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: 119.32  E-value: 2.20e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2CC3_A        5 TQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPqVILGKHGRLEVEHIA-SNDVTP 83
Cdd:cd16424   1 TYDEALDKYFLAQYVRARESYDWATLQEDYDTVRLMSSPDVAAEYRALFNGDNPPSP-KVLGKNARVEVKILSiSFLGGD 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
2CC3_A       84 GVQQIRYKRTLI-VDGKMPMASTWTATVRYEKVTS-LPGRLRLTNPGGLVVTSYQTSE 139
Cdd:cd16424  80 NTAQVRFTKTIRdKGGGEPTPTYWIATITFDYVPApMTEEDRLINPLGFQVTSYRVDP 137
 
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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