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Conserved domains on  [gi|510921941|ref|WP_016242740|]
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type VI secretion system tube protein TssD [Escherichia coli]

Protein Classification

HNH endonuclease( domain architecture ID 11632653)

HNH endonuclease signature motif containing protein catalyzes the hydrolysis of DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pyocin_S pfam06958
S-type Pyocin; This family represents a conserved region approximately 180 residues long ...
 309-450 1.63e-45

S-type Pyocin; This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.


:

Pssm-ID: 399737  Cd Length: 139  Bit Score: 157.53  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941  309 LRQKALAGSTATTRVRFFWGTDIHGKPQVYGVHTGEGTPYENVRVANMQWNEQTQRYEFTpAHDVDGPLITWTPENPEhG 388
Cdd:pfam06958   1 LEEIAAQMGTVDLPVRLRIIDDEDGRLKVYGVHTGGAGVPDRVPVRAATLDAETGSYEFT-ADGAPGPTILWTPASPP-G 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 510921941  389 NVPGHTGNDRPPLDQPTILVTPIPDGTDTYTTpPFPVPDPKEFNDYILVFPAGSGIKPIYVY 450
Cdd:pfam06958  79 NGPPSTSSPAAPPDTPVITGTPIPPVVGEVIE-PYPAPDERDFRDYILVFPADSGLPPLYVV 139
T6SS_HCP super family cl01226
Type VI secretion system effector, Hcp; HCP is a family of proteins which are expressed in up ...
 4-148 1.05e-40

Type VI secretion system effector, Hcp; HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube.


The actual alignment was detected with superfamily member TIGR03344:

Pssm-ID: 470123  Cd Length: 166  Bit Score: 145.17  E-value: 1.05e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941    4 IVYLRIIGEKQGDISSGCGTYASVGNRWQVGHEDEIFAFALTNAIT--------STGKGVNLQGLQFCKLIDKSSPLLSN 75
Cdd:TIGR03344   3 PIYLTITGKTQGLISAGCSTADSIGNKYQEGHEDEIMVLAFDHSISrpqnpqsgLPTGRVVHQPIVITKPIDKSSPLLYQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941   76 AINQNERL-FIEIDLYRINKSGRWERYYYIQLRNASLTAI-----HVNISDNNLPTECVTVDYDYILCKHLIANTEF--D 147
Cdd:TIGR03344  83 ALSSGEKLeECEIKFYRTSAAGKQELYYTIKLEGALIVDIkpympHCLDPNNAQPLEDVSFRYRKITWTHHIAGTSGysS 162


                  .
gi 510921941  148 W 148
Cdd:TIGR03344 163 W 163
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 550-590 8.25e-06

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


:

Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 43.23  E-value: 8.25e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 510921941 550 GPKEIVKKFQIHHRVAIEYGGSvYDIDNLRIVTPRLHDEIH 590
Cdd:cd00085   18 GKPGGTEGLEVDHIIPLSDGGN-NDLDNLVLLCRKCHRKKH 57
 
Name Accession Description Interval E-value
Pyocin_S pfam06958
S-type Pyocin; This family represents a conserved region approximately 180 residues long ...
 309-450 1.63e-45

S-type Pyocin; This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.


Pssm-ID: 399737  Cd Length: 139  Bit Score: 157.53  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941  309 LRQKALAGSTATTRVRFFWGTDIHGKPQVYGVHTGEGTPYENVRVANMQWNEQTQRYEFTpAHDVDGPLITWTPENPEhG 388
Cdd:pfam06958   1 LEEIAAQMGTVDLPVRLRIIDDEDGRLKVYGVHTGGAGVPDRVPVRAATLDAETGSYEFT-ADGAPGPTILWTPASPP-G 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 510921941  389 NVPGHTGNDRPPLDQPTILVTPIPDGTDTYTTpPFPVPDPKEFNDYILVFPAGSGIKPIYVY 450
Cdd:pfam06958  79 NGPPSTSSPAAPPDTPVITGTPIPPVVGEVIE-PYPAPDERDFRDYILVFPADSGLPPLYVV 139
VI_effect_Hcp1 TIGR03344
type VI secretion system effector, Hcp1 family; This family includes Hcp1 (hemolysin ...
 4-148 1.05e-40

type VI secretion system effector, Hcp1 family; This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens. [Cellular processes, Pathogenesis]


Pssm-ID: 213799  Cd Length: 166  Bit Score: 145.17  E-value: 1.05e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941    4 IVYLRIIGEKQGDISSGCGTYASVGNRWQVGHEDEIFAFALTNAIT--------STGKGVNLQGLQFCKLIDKSSPLLSN 75
Cdd:TIGR03344   3 PIYLTITGKTQGLISAGCSTADSIGNKYQEGHEDEIMVLAFDHSISrpqnpqsgLPTGRVVHQPIVITKPIDKSSPLLYQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941   76 AINQNERL-FIEIDLYRINKSGRWERYYYIQLRNASLTAI-----HVNISDNNLPTECVTVDYDYILCKHLIANTEF--D 147
Cdd:TIGR03344  83 ALSSGEKLeECEIKFYRTSAAGKQELYYTIKLEGALIVDIkpympHCLDPNNAQPLEDVSFRYRKITWTHHIAGTSGysS 162


                  .
gi 510921941  148 W 148
Cdd:TIGR03344 163 W 163
T6SS_HCP pfam05638
Type VI secretion system effector, Hcp; HCP is a family of proteins which are expressed in up ...
 28-139 3.40e-14

Type VI secretion system effector, Hcp; HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube.


Pssm-ID: 428557  Cd Length: 129  Bit Score: 69.48  E-value: 3.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941   28 GNRWQVGHEDEI----FAFALTNAI-----TSTGKG---VNLQGLQFCKLIDKSSPLLSNAINQNERLF-IEIDLYRINK 94
Cdd:pfam05638   9 GESTDAGHEDWIevlsFSHGVSQPTdsntgSGTGRRagkVSHSPLTFTKEIDKASPLLYKACATGEHLKtVELTFYRASG 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 510921941   95 SGRwERYYYIQLRNASLTAIHVNisdNNLPTECVTVDYDYILCKH 139
Cdd:pfam05638  89 GKE-EEYLTITLEDVIISSVSPS---GMRPTESVSLSYAKITWTY 129
Hcp COG3157
Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, ...
 28-148 1.07e-11

Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442391  Cd Length: 162  Bit Score: 63.35  E-value: 1.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941  28 GNRWQVGHEDEI----FAFALTNAI---TSTGKG-----VNLQGLQFCKLIDKSSPLLSNAINQNERLF-IEIDLYRINk 94
Cdd:COG3157   14 GESTDKGHEGWIevlsFSHGVSQPTdgtTSSGGGrgagkRSHSDLTFTKEIDKASPLLYKACASGKHLKkAELKFYRAN- 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 510921941  95 SGRWERYYYIQLRNASLTAIHVNISDNN-LPTECVT-----VDYDYILCK---HLIANTEFDW 148
Cdd:COG3157   93 GGKEEEYLTITLENVIISSVSPSGSGGEgTPLETVSlsyakITWTYTPQDadgGIGGEVTDGW 155
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 550-590 8.25e-06

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 43.23  E-value: 8.25e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 510921941 550 GPKEIVKKFQIHHRVAIEYGGSvYDIDNLRIVTPRLHDEIH 590
Cdd:cd00085   18 GKPGGTEGLEVDHIIPLSDGGN-NDLDNLVLLCRKCHRKKH 57
 
Name Accession Description Interval E-value
Pyocin_S pfam06958
S-type Pyocin; This family represents a conserved region approximately 180 residues long ...
 309-450 1.63e-45

S-type Pyocin; This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.


Pssm-ID: 399737  Cd Length: 139  Bit Score: 157.53  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941  309 LRQKALAGSTATTRVRFFWGTDIHGKPQVYGVHTGEGTPYENVRVANMQWNEQTQRYEFTpAHDVDGPLITWTPENPEhG 388
Cdd:pfam06958   1 LEEIAAQMGTVDLPVRLRIIDDEDGRLKVYGVHTGGAGVPDRVPVRAATLDAETGSYEFT-ADGAPGPTILWTPASPP-G 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 510921941  389 NVPGHTGNDRPPLDQPTILVTPIPDGTDTYTTpPFPVPDPKEFNDYILVFPAGSGIKPIYVY 450
Cdd:pfam06958  79 NGPPSTSSPAAPPDTPVITGTPIPPVVGEVIE-PYPAPDERDFRDYILVFPADSGLPPLYVV 139
VI_effect_Hcp1 TIGR03344
type VI secretion system effector, Hcp1 family; This family includes Hcp1 (hemolysin ...
 4-148 1.05e-40

type VI secretion system effector, Hcp1 family; This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens. [Cellular processes, Pathogenesis]


Pssm-ID: 213799  Cd Length: 166  Bit Score: 145.17  E-value: 1.05e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941    4 IVYLRIIGEKQGDISSGCGTYASVGNRWQVGHEDEIFAFALTNAIT--------STGKGVNLQGLQFCKLIDKSSPLLSN 75
Cdd:TIGR03344   3 PIYLTITGKTQGLISAGCSTADSIGNKYQEGHEDEIMVLAFDHSISrpqnpqsgLPTGRVVHQPIVITKPIDKSSPLLYQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941   76 AINQNERL-FIEIDLYRINKSGRWERYYYIQLRNASLTAI-----HVNISDNNLPTECVTVDYDYILCKHLIANTEF--D 147
Cdd:TIGR03344  83 ALSSGEKLeECEIKFYRTSAAGKQELYYTIKLEGALIVDIkpympHCLDPNNAQPLEDVSFRYRKITWTHHIAGTSGysS 162


                  .
gi 510921941  148 W 148
Cdd:TIGR03344 163 W 163
T6SS_HCP pfam05638
Type VI secretion system effector, Hcp; HCP is a family of proteins which are expressed in up ...
 28-139 3.40e-14

Type VI secretion system effector, Hcp; HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube.


Pssm-ID: 428557  Cd Length: 129  Bit Score: 69.48  E-value: 3.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941   28 GNRWQVGHEDEI----FAFALTNAI-----TSTGKG---VNLQGLQFCKLIDKSSPLLSNAINQNERLF-IEIDLYRINK 94
Cdd:pfam05638   9 GESTDAGHEDWIevlsFSHGVSQPTdsntgSGTGRRagkVSHSPLTFTKEIDKASPLLYKACATGEHLKtVELTFYRASG 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 510921941   95 SGRwERYYYIQLRNASLTAIHVNisdNNLPTECVTVDYDYILCKH 139
Cdd:pfam05638  89 GKE-EEYLTITLEDVIISSVSPS---GMRPTESVSLSYAKITWTY 129
Hcp COG3157
Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, ...
 28-148 1.07e-11

Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442391  Cd Length: 162  Bit Score: 63.35  E-value: 1.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510921941  28 GNRWQVGHEDEI----FAFALTNAI---TSTGKG-----VNLQGLQFCKLIDKSSPLLSNAINQNERLF-IEIDLYRINk 94
Cdd:COG3157   14 GESTDKGHEGWIevlsFSHGVSQPTdgtTSSGGGrgagkRSHSDLTFTKEIDKASPLLYKACASGKHLKkAELKFYRAN- 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 510921941  95 SGRWERYYYIQLRNASLTAIHVNISDNN-LPTECVT-----VDYDYILCK---HLIANTEFDW 148
Cdd:COG3157   93 GGKEEEYLTITLENVIISSVSPSGSGGEgTPLETVSlsyakITWTYTPQDadgGIGGEVTDGW 155
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 550-590 8.25e-06

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 43.23  E-value: 8.25e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 510921941 550 GPKEIVKKFQIHHRVAIEYGGSvYDIDNLRIVTPRLHDEIH 590
Cdd:cd00085   18 GKPGGTEGLEVDHIIPLSDGGN-NDLDNLVLLCRKCHRKKH 57
 
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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