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Conserved domains on  [gi|2176067508|ref|WP_234009644|]
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phage baseplate assembly protein V, partial [Cronobacter malonaticus]

Protein Classification

type VI secretion system Vgr family protein( domain architecture ID 1002305)

type VI secretion system Vgr family protein; type VI secretion system tip protein VgrG is a core component and effector of Type VI secretion systems (T6SSs) that are involved in the pathogenicity of several Gram-negative bacteria

CATH:  2.30.110.50
Gene Ontology:  GO:0033104|GO:0033103
PubMed:  27352036

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VgrG super family cl34624
Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly ...
 1-225 1.91e-56

Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly [Intracellular trafficking, secretion, and vesicular transport, Mobilome: prophages, transposons, General function prediction only];


The actual alignment was detected with superfamily member COG3501:

Pssm-ID: 442724 [Multi-domain]  Cd Length: 743  Bit Score: 190.74  E-value: 1.91e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508   1 GGVQIPRVGDEVVVDFINGDPDRPLITGRVYNEASMPPWALPAAATQMGFLSRSKDGspDNANALRFEDKAGEEQVWLQA 80
Cdd:COG3501   422 GGHFIPRVGQEVLVAFLDGDPDRPIVTGRVYNGANMPPYTLPANKTRSGIRTRSSPG--GGFNELRFDDKAGQEEIFLHA 499

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508  81 ERNLDTKVKKDETHSVGGSRILSVKQDYTGKVEGKQEHAIQMSRNELVGGQYDIKGQGTVTVSSATGIRLVTGDSVLEMS 160
Cdd:COG3501   500 EKDMNTLVDNDETITVGNDRTEEVGTDETGTVAGNQGLTVSGDQTVVVGGNQTLVVGGARTLVVGGNLAAVVGGAAATAG 579

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2176067508 161 ANGEVNLYCTKFAINASGTGQINTGGTLDLNLKKEPDKASNVAPTPGDIQNEVAKTFNSDGEGQA 225
Cdd:COG3501   580 GAQATLVAGALLLLAAGGALTTVGGGGTTTGGGAAATAGGGGAGAAAGGAATAAAGAAATSAAGG 644
 
Name Accession Description Interval E-value
VgrG COG3501
Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly ...
 1-225 1.91e-56

Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly [Intracellular trafficking, secretion, and vesicular transport, Mobilome: prophages, transposons, General function prediction only];


Pssm-ID: 442724 [Multi-domain]  Cd Length: 743  Bit Score: 190.74  E-value: 1.91e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508   1 GGVQIPRVGDEVVVDFINGDPDRPLITGRVYNEASMPPWALPAAATQMGFLSRSKDGspDNANALRFEDKAGEEQVWLQA 80
Cdd:COG3501   422 GGHFIPRVGQEVLVAFLDGDPDRPIVTGRVYNGANMPPYTLPANKTRSGIRTRSSPG--GGFNELRFDDKAGQEEIFLHA 499

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508  81 ERNLDTKVKKDETHSVGGSRILSVKQDYTGKVEGKQEHAIQMSRNELVGGQYDIKGQGTVTVSSATGIRLVTGDSVLEMS 160
Cdd:COG3501   500 EKDMNTLVDNDETITVGNDRTEEVGTDETGTVAGNQGLTVSGDQTVVVGGNQTLVVGGARTLVVGGNLAAVVGGAAATAG 579

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2176067508 161 ANGEVNLYCTKFAINASGTGQINTGGTLDLNLKKEPDKASNVAPTPGDIQNEVAKTFNSDGEGQA 225
Cdd:COG3501   580 GAQATLVAGALLLLAAGGALTTVGGGGTTTGGGAAATAGGGGAGAAAGGAATAAAGAAATSAAGG 644
VI_Rhs_Vgr TIGR03361
type VI secretion system Vgr family protein; Members of this protein family belong to the Rhs ...
 1-100 4.14e-56

type VI secretion system Vgr family protein; Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.


Pssm-ID: 274542 [Multi-domain]  Cd Length: 513  Bit Score: 185.87  E-value: 4.14e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508   1 GGVQIPRVGDEVVVDFINGDPDRPLITGRVYNEASMPPWALPAAATQMGFLSRSKDGSpDNANALRFEDKAGEEQVWLQA 80
Cdd:TIGR03361 414 GSVAIPRVGQEVVVDFLEGDPDRPIVTGRVYNAENMPPYSLPANKTQSGFRSRSSKGG-GGFNELRFEDKAGAEEIYLHA 492

                          90       100
                  ....*....|....*....|
gi 2176067508  81 ERNLDTKVKKDETHSVGGSR 100
Cdd:TIGR03361 493 QRDMNTEVENDSTHTVGNNR 512
Phage_base_V pfam04717
Type VI secretion system/phage-baseplate injector OB domain; Family of bacterial and phage ...
 5-31 8.60e-05

Type VI secretion system/phage-baseplate injector OB domain; Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft. This entry represents the OB fold part of the structure. This structure contains an unusual extra beta hairpin that forms the foundation of the spike protein's beta helix.


Pssm-ID: 428084 [Multi-domain]  Cd Length: 75  Bit Score: 39.87  E-value: 8.60e-05
                          10        20
                  ....*....|....*....|....*..
gi 2176067508   5 IPRVGDEVVVDFINGDPDRPLITGRVY 31
Cdd:pfam04717  49 LPEVGEQVLVLFEGGDPSRPVVLGGLW 75
 
Name Accession Description Interval E-value
VgrG COG3501
Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly ...
 1-225 1.91e-56

Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly [Intracellular trafficking, secretion, and vesicular transport, Mobilome: prophages, transposons, General function prediction only];


Pssm-ID: 442724 [Multi-domain]  Cd Length: 743  Bit Score: 190.74  E-value: 1.91e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508   1 GGVQIPRVGDEVVVDFINGDPDRPLITGRVYNEASMPPWALPAAATQMGFLSRSKDGspDNANALRFEDKAGEEQVWLQA 80
Cdd:COG3501   422 GGHFIPRVGQEVLVAFLDGDPDRPIVTGRVYNGANMPPYTLPANKTRSGIRTRSSPG--GGFNELRFDDKAGQEEIFLHA 499

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508  81 ERNLDTKVKKDETHSVGGSRILSVKQDYTGKVEGKQEHAIQMSRNELVGGQYDIKGQGTVTVSSATGIRLVTGDSVLEMS 160
Cdd:COG3501   500 EKDMNTLVDNDETITVGNDRTEEVGTDETGTVAGNQGLTVSGDQTVVVGGNQTLVVGGARTLVVGGNLAAVVGGAAATAG 579

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2176067508 161 ANGEVNLYCTKFAINASGTGQINTGGTLDLNLKKEPDKASNVAPTPGDIQNEVAKTFNSDGEGQA 225
Cdd:COG3501   580 GAQATLVAGALLLLAAGGALTTVGGGGTTTGGGAAATAGGGGAGAAAGGAATAAAGAAATSAAGG 644
VI_Rhs_Vgr TIGR03361
type VI secretion system Vgr family protein; Members of this protein family belong to the Rhs ...
 1-100 4.14e-56

type VI secretion system Vgr family protein; Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.


Pssm-ID: 274542 [Multi-domain]  Cd Length: 513  Bit Score: 185.87  E-value: 4.14e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508   1 GGVQIPRVGDEVVVDFINGDPDRPLITGRVYNEASMPPWALPAAATQMGFLSRSKDGSpDNANALRFEDKAGEEQVWLQA 80
Cdd:TIGR03361 414 GSVAIPRVGQEVVVDFLEGDPDRPIVTGRVYNAENMPPYSLPANKTQSGFRSRSSKGG-GGFNELRFEDKAGAEEIYLHA 492

                          90       100
                  ....*....|....*....|
gi 2176067508  81 ERNLDTKVKKDETHSVGGSR 100
Cdd:TIGR03361 493 QRDMNTEVENDSTHTVGNNR 512
vgr_GE TIGR01646
Rhs element Vgr protein; This model represents the Vgr family of proteins, associated with ...
 1-83 8.58e-32

Rhs element Vgr protein; This model represents the Vgr family of proteins, associated with some classes of Rhs elements. This model does not include a large octapeptide repeat region, VGXXXXXX, found in the Vgr of Rhs classes G and E.


Pssm-ID: 273730 [Multi-domain]  Cd Length: 483  Bit Score: 120.66  E-value: 8.58e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2176067508   1 GGVQIPRVGDEVVVDFINGDPDRPLITGRVYNEASMPPWALPAAATQMGFLSRSKDGSpdNANALRFEDKAGEEQVWLQA 80
Cdd:TIGR01646 403 GSLAIPRVGQEVIVGFLDGDPDRPIVTGRVYNAANPPPYRLPAHNTQSGFKSRTLRGG--SQNQLRFDDDKGKEQLQLHA 480


                  ...
gi 2176067508  81 ERN 83
Cdd:TIGR01646 481 ERD 483
Phage_base_V pfam04717
Type VI secretion system/phage-baseplate injector OB domain; Family of bacterial and phage ...
 5-31 8.60e-05

Type VI secretion system/phage-baseplate injector OB domain; Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft. This entry represents the OB fold part of the structure. This structure contains an unusual extra beta hairpin that forms the foundation of the spike protein's beta helix.


Pssm-ID: 428084 [Multi-domain]  Cd Length: 75  Bit Score: 39.87  E-value: 8.60e-05
                          10        20
                  ....*....|....*....|....*..
gi 2176067508   5 IPRVGDEVVVDFINGDPDRPLITGRVY 31
Cdd:pfam04717  49 LPEVGEQVLVLFEGGDPSRPVVLGGLW 75
DUF6484 pfam20093
Domain of unknown function (DUF6484); This domain of unknown function is found in ...
 8-30 2.66e-04

Domain of unknown function (DUF6484); This domain of unknown function is found in uncharacterized proteins from Proteobacteria. This domain is approximately 80 amino acids in length and exhibits overlaps with pfam04717, which suggests that it has an OB fold and, thus, it belongs to the same clan. Many proteins containing this domain are related to the Type VI secretion system and to Phage-related baseplate proteins.


Pssm-ID: 466287 [Multi-domain]  Cd Length: 61  Bit Score: 37.93  E-value: 2.66e-04
                          10        20
                  ....*....|....*....|...
gi 2176067508   8 VGDEVVVDFINGDPDRPLITGRV 30
Cdd:pfam20093  39 LGREVALLFEDGDPRRPLIMGLL 61
 
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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