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Conserved domains on  [gi|1239385679|ref|WP_095450939|]
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MULTISPECIES: relaxosome protein TraM [Enterobacteriaceae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tra_M super family cl23827
TraM mediates signalling between transferosome and relaxosome; TraM is a plasmid encoded ...
 1-115 1.05e-36

TraM mediates signalling between transferosome and relaxosome; TraM is a plasmid encoded DNA-binding protein that is essential for conjugative transfer of F-like plasmids (e.g. F, R1, R100 and pED208) between bacterial cells. Bacterial conjugation, a form of horizontal gene transfer between cells, is an important contributor to bacterial genetic diversity, enabling virulence and antibiotics resistance factors to rapidly spread in medically important human pathogens. Mutation studies have shown that TraM is required for normal levels of transfer gene expression as well as for efficient site-specific single-stranded DNA cleavage at the origin of transfer (oriT). TraM tetramers bridge oriT to a key component of the conjugative pore, the coupling protein TraD. The N-terminal ribbon-helix-helix (RHH) domain of TraM is able to cooperatively bind DNA in a staggered arrangement without interaction between tetramers. This allows the C-terminal TraM tetramerization domains to be free to make multiple interactions with TraD, thus driving plasmid recruitment to the conjugative pore.


The actual alignment was detected with superfamily member cd14804:

Pssm-ID: 420037  Cd Length: 122  Bit Score: 121.21  E-value: 1.05e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1239385679   1 MPRKNIYFKDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVYKSKEE--GSSFDLDGFRRDLIKKVSGSREG 78
Cdd:cd14804     1 MPRVQIYVKQKVLEEIRDIVDERIQEGATPAEANISSVCSELLELGLRVYEAQQEkkESGFNQMEFNKLLLENVLKTRFL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1239385679  79 IMILTALVSDIF-----VTLKGPESGVKLEELINTNISAIND 115
Cdd:cd14804    81 VQKILAMMSELQeikedSRFNYEEIKEAIKELIQEKLSAFFP 122
 
Name Accession Description Interval E-value
Tra_M cd14804
TraM mediates signalling between transferosome and relaxosome; TraM is a plasmid encoded ...
 1-115 1.05e-36

TraM mediates signalling between transferosome and relaxosome; TraM is a plasmid encoded DNA-binding protein that is essential for conjugative transfer of F-like plasmids (e.g. F, R1, R100 and pED208) between bacterial cells. Bacterial conjugation, a form of horizontal gene transfer between cells, is an important contributor to bacterial genetic diversity, enabling virulence and antibiotics resistance factors to rapidly spread in medically important human pathogens. Mutation studies have shown that TraM is required for normal levels of transfer gene expression as well as for efficient site-specific single-stranded DNA cleavage at the origin of transfer (oriT). TraM tetramers bridge oriT to a key component of the conjugative pore, the coupling protein TraD. The N-terminal ribbon-helix-helix (RHH) domain of TraM is able to cooperatively bind DNA in a staggered arrangement without interaction between tetramers. This allows the C-terminal TraM tetramerization domains to be free to make multiple interactions with TraD, thus driving plasmid recruitment to the conjugative pore.


Pssm-ID: 271351  Cd Length: 122  Bit Score: 121.21  E-value: 1.05e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1239385679   1 MPRKNIYFKDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVYKSKEE--GSSFDLDGFRRDLIKKVSGSREG 78
Cdd:cd14804     1 MPRVQIYVKQKVLEEIRDIVDERIQEGATPAEANISSVCSELLELGLRVYEAQQEkkESGFNQMEFNKLLLENVLKTRFL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1239385679  79 IMILTALVSDIF-----VTLKGPESGVKLEELINTNISAIND 115
Cdd:cd14804    81 VQKILAMMSELQeikedSRFNYEEIKEAIKELIQEKLSAFFP 122
PRK13713 PRK13713
relaxosome protein TraM;
9-89 4.10e-08

relaxosome protein TraM;


Pssm-ID: 184269  Cd Length: 118  Bit Score: 48.13  E-value: 4.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1239385679   9 KDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVY----KSKEEGssFDLDGFRRDLIKKVSGSRE------G 78
Cdd:PRK13713    2 SNEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYeaqmERKESG--FNQTEFNKLLLECVVKTQStvakilG 79

                          90
                  ....*....|.
gi 1239385679  79 IMILTALVSDI 89
Cdd:PRK13713   80 IESLSPHVSGN 90
Tra_M pfam05261
TraM protein, DNA-binding; The TraM protein is an essential part of the DNA transfer machinery ...
 1-72 2.27e-05

TraM protein, DNA-binding; The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus.


Pssm-ID: 398777  Cd Length: 126  Bit Score: 41.17  E-value: 2.27e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1239385679   1 MPRKNIYFKDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVYKSKEE--GSSFDLDGFRRDLIKKV 72
Cdd:pfam05261   1 MAKINAYISDEVAEKINAIVEKRKAEGARDKDISFSGTSSMLLELGLRVYEAQMErkESGFNQMAFNKVLLENV 74
 
Name Accession Description Interval E-value
Tra_M cd14804
TraM mediates signalling between transferosome and relaxosome; TraM is a plasmid encoded ...
 1-115 1.05e-36

TraM mediates signalling between transferosome and relaxosome; TraM is a plasmid encoded DNA-binding protein that is essential for conjugative transfer of F-like plasmids (e.g. F, R1, R100 and pED208) between bacterial cells. Bacterial conjugation, a form of horizontal gene transfer between cells, is an important contributor to bacterial genetic diversity, enabling virulence and antibiotics resistance factors to rapidly spread in medically important human pathogens. Mutation studies have shown that TraM is required for normal levels of transfer gene expression as well as for efficient site-specific single-stranded DNA cleavage at the origin of transfer (oriT). TraM tetramers bridge oriT to a key component of the conjugative pore, the coupling protein TraD. The N-terminal ribbon-helix-helix (RHH) domain of TraM is able to cooperatively bind DNA in a staggered arrangement without interaction between tetramers. This allows the C-terminal TraM tetramerization domains to be free to make multiple interactions with TraD, thus driving plasmid recruitment to the conjugative pore.


Pssm-ID: 271351  Cd Length: 122  Bit Score: 121.21  E-value: 1.05e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1239385679   1 MPRKNIYFKDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVYKSKEE--GSSFDLDGFRRDLIKKVSGSREG 78
Cdd:cd14804     1 MPRVQIYVKQKVLEEIRDIVDERIQEGATPAEANISSVCSELLELGLRVYEAQQEkkESGFNQMEFNKLLLENVLKTRFL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1239385679  79 IMILTALVSDIF-----VTLKGPESGVKLEELINTNISAIND 115
Cdd:cd14804    81 VQKILAMMSELQeikedSRFNYEEIKEAIKELIQEKLSAFFP 122
PRK13713 PRK13713
relaxosome protein TraM;
9-89 4.10e-08

relaxosome protein TraM;


Pssm-ID: 184269  Cd Length: 118  Bit Score: 48.13  E-value: 4.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1239385679   9 KDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVY----KSKEEGssFDLDGFRRDLIKKVSGSRE------G 78
Cdd:PRK13713    2 SNEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYeaqmERKESG--FNQTEFNKLLLECVVKTQStvakilG 79

                          90
                  ....*....|.
gi 1239385679  79 IMILTALVSDI 89
Cdd:PRK13713   80 IESLSPHVSGN 90
Tra_M pfam05261
TraM protein, DNA-binding; The TraM protein is an essential part of the DNA transfer machinery ...
 1-72 2.27e-05

TraM protein, DNA-binding; The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus.


Pssm-ID: 398777  Cd Length: 126  Bit Score: 41.17  E-value: 2.27e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1239385679   1 MPRKNIYFKDKIDREIHDILEIELQKGATSSEMNYSSIVNELVRLGLMVYKSKEE--GSSFDLDGFRRDLIKKV 72
Cdd:pfam05261   1 MAKINAYISDEVAEKINAIVEKRKAEGARDKDISFSGTSSMLLELGLRVYEAQMErkESGFNQMAFNKVLLENV 74
 
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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