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Conserved domains on  [gi|1949532433|ref|WP_198548839|]
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hypothetical protein, partial [Escherichia coli]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK14712 super family cl36417
conjugal transfer nickase/helicase TraI; Provisional
 1-73 9.38e-43

conjugal transfer nickase/helicase TraI; Provisional


The actual alignment was detected with superfamily member PRK14712:

Pssm-ID: 237796 [Multi-domain]  Cd Length: 1623  Bit Score: 146.54  E-value: 9.38e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1949532433    1 PGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 73
Cdd:PRK14712   519 PGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 591
 
Name Accession Description Interval E-value
PRK14712 PRK14712
conjugal transfer nickase/helicase TraI; Provisional
 1-73 9.38e-43

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237796 [Multi-domain]  Cd Length: 1623  Bit Score: 146.54  E-value: 9.38e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1949532433    1 PGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 73
Cdd:PRK14712   519 PGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 591
TraI_TIGR TIGR02760
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ...
 2-73 7.98e-30

conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.


Pssm-ID: 274285 [Multi-domain]  Cd Length: 1960  Bit Score: 109.61  E-value: 7.98e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1949532433    2 GMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSL---DSSWSLFRPEKMPVADGERLRVTGKI 73
Cdd:TIGR02760  685 GMVIRFWQKGKIPHDDYVVTNVNKHNNTLTLKDAQGKTQKFKPSSLkdlERPFSVYRPEQLEVAAGERLQVTGNH 759
TraI_2B pfam18340
DNA relaxase TraI 2B/2B-like domain; This is the 2B and 2B-like sub-domain found in TraI (EC:5. ...
 1-61 3.13e-26

DNA relaxase TraI 2B/2B-like domain; This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components. The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system.


Pssm-ID: 465718 [Multi-domain]  Cd Length: 79  Bit Score: 91.18  E-value: 3.13e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1949532433  1 PGMVMEQWNPeTRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPV 61
Cdd:pfam18340 20 EGMVLERWNG-ARKKQRFTIDRVTEKTNSLTLVDAKGETSTLKISEIDSHWRLFRSDKLEV 79
 
Name Accession Description Interval E-value
PRK14712 PRK14712
conjugal transfer nickase/helicase TraI; Provisional
 1-73 9.38e-43

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237796 [Multi-domain]  Cd Length: 1623  Bit Score: 146.54  E-value: 9.38e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1949532433    1 PGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 73
Cdd:PRK14712   519 PGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 591
PRK13709 PRK13709
conjugal transfer nickase/helicase TraI; Provisional
 1-73 1.20e-40

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237478 [Multi-domain]  Cd Length: 1747  Bit Score: 140.31  E-value: 1.20e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1949532433    1 PGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 73
Cdd:PRK13709   651 PGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVKISSLDSSWSLFRPEKMPVADGERLRVLGKI 723
TraI_TIGR TIGR02760
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ...
 2-73 7.98e-30

conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.


Pssm-ID: 274285 [Multi-domain]  Cd Length: 1960  Bit Score: 109.61  E-value: 7.98e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1949532433    2 GMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSL---DSSWSLFRPEKMPVADGERLRVTGKI 73
Cdd:TIGR02760  685 GMVIRFWQKGKIPHDDYVVTNVNKHNNTLTLKDAQGKTQKFKPSSLkdlERPFSVYRPEQLEVAAGERLQVTGNH 759
TraI_2B pfam18340
DNA relaxase TraI 2B/2B-like domain; This is the 2B and 2B-like sub-domain found in TraI (EC:5. ...
 1-61 3.13e-26

DNA relaxase TraI 2B/2B-like domain; This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components. The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system.


Pssm-ID: 465718 [Multi-domain]  Cd Length: 79  Bit Score: 91.18  E-value: 3.13e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1949532433  1 PGMVMEQWNPeTRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPV 61
Cdd:pfam18340 20 EGMVLERWNG-ARKKQRFTIDRVTEKTNSLTLVDAKGETSTLKISEIDSHWRLFRSDKLEV 79
PRK13709 PRK13709
conjugal transfer nickase/helicase TraI; Provisional
 5-70 1.14e-03

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237478 [Multi-domain]  Cd Length: 1747  Bit Score: 35.15  E-value: 1.14e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1949532433    5 MEQWNPETRS----HDRYV-IDRVTAQSHSLTLRDAQGETQVVRISSLDSS-WSLFRPEKMPVADGERLRVT 70
Cdd:PRK13709  1273 LSTWEAHRGAlalvDNVYHrIAGIDKDDGLITLRDAEGNTRLISPREAVAEgVTLYTPDTIRVGTGDRMRFT 1344
 
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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