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Conserved domains on  [gi|1633648422|gb|TKI34387|]
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DNA-binding protein [Klebsiella variicola]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaT super family cl46275
DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain ...
 172-261 2.73e-28

DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in Swiss:P0A8J2 can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N- and C- terminals are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to pfam08585 except that it contains an extra loop at the N-terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilization of the three-helix bundle.


The actual alignment was detected with superfamily member PRK02854:

Pssm-ID: 480615  Cd Length: 179  Bit Score: 107.97  E-value: 2.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1633648422 172 NQPGIVPgetqaFGKFAMYFGWKPSEDFPRLATIWGMPLRPGInLAAELSSFIAYWQAEGRAFHQVQWEQKLARHL--NR 249
Cdd:PRK02854   79 AAPVAVP-----MGKFAMYPDWQPDADFIRQAALWGVALREPV-TAEELASFIAYWQAEGKVFHHIQWQQKLARSLqiSR 152

                          90
                  ....*....|....
gi 1633648422 250 AE--VRQKKPVNGV 261
Cdd:PRK02854  153 ASngGQPKRDINTV 166
HTH_36 pfam13730
Helix-turn-helix domain;
11-62 1.27e-06

Helix-turn-helix domain;


:

Pssm-ID: 463970 [Multi-domain]  Cd Length: 55  Bit Score: 44.79  E-value: 1.27e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1633648422  11 KSSAKAVLTWMADMCGADLCAFPSIPALAEATELDKKTVQSSLQYLVSIGLI 62
Cdd:pfam13730   4 SPTAKLLLLILASYANKDGGCFPSVETLAKRLGLSRRTIQRAIKELEELGYL 55
 
Name Accession Description Interval E-value
PRK02854 PRK02854
primosomal protein DnaT;
172-261 2.73e-28

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 107.97  E-value: 2.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1633648422 172 NQPGIVPgetqaFGKFAMYFGWKPSEDFPRLATIWGMPLRPGInLAAELSSFIAYWQAEGRAFHQVQWEQKLARHL--NR 249
Cdd:PRK02854   79 AAPVAVP-----MGKFAMYPDWQPDADFIRQAALWGVALREPV-TAEELASFIAYWQAEGKVFHHIQWQQKLARSLqiSR 152

                          90
                  ....*....|....
gi 1633648422 250 AE--VRQKKPVNGV 261
Cdd:PRK02854  153 ASngGQPKRDINTV 166
DnaT pfam17948
DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain ...
 187-259 1.87e-16

DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in Swiss:P0A8J2 can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N- and C- terminals are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to pfam08585 except that it contains an extra loop at the N-terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilization of the three-helix bundle.


Pssm-ID: 465580  Cd Length: 69  Bit Score: 72.67  E-value: 1.87e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1633648422 187 FAMYFGWKPSEDFPRLATIWGMPLRPGINlaAELSSFIAYWQAEGraFHQVQWEQKLARHLNRAEVRQKKPVN 259
Cdd:pfam17948   1 FPMHLDWQPSADFLEILALAGGIDRDFAE--DELPEFVLYWRERG--FAQHQWNQKFVQHVKRQWARYQSSLG 69
ECs1768 COG5529
Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: ...
 199-269 1.66e-07

Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: prophages, transposons];


Pssm-ID: 444280  Cd Length: 104  Bit Score: 48.72  E-value: 1.66e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1633648422 199 FPRLATIWGMPLrpginlaAELSSFIAYWQAEGRAFHQvqwEQKLARHLNRAE-VRQKKPVNGVNDHVGVRA 269
Cdd:COG5529     1 FSRQAALWGIAL-------PELAAFRAHWQKHGKEFGS---QQKLARYVQQARaFVNRPPRRDRGTLTKTRP 62
HTH_36 pfam13730
Helix-turn-helix domain;
11-62 1.27e-06

Helix-turn-helix domain;


Pssm-ID: 463970 [Multi-domain]  Cd Length: 55  Bit Score: 44.79  E-value: 1.27e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1633648422  11 KSSAKAVLTWMADMCGADLCAFPSIPALAEATELDKKTVQSSLQYLVSIGLI 62
Cdd:pfam13730   4 SPTAKLLLLILASYANKDGGCFPSVETLAKRLGLSRRTIQRAIKELEELGYL 55
 
Name Accession Description Interval E-value
PRK02854 PRK02854
primosomal protein DnaT;
172-261 2.73e-28

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 107.97  E-value: 2.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1633648422 172 NQPGIVPgetqaFGKFAMYFGWKPSEDFPRLATIWGMPLRPGInLAAELSSFIAYWQAEGRAFHQVQWEQKLARHL--NR 249
Cdd:PRK02854   79 AAPVAVP-----MGKFAMYPDWQPDADFIRQAALWGVALREPV-TAEELASFIAYWQAEGKVFHHIQWQQKLARSLqiSR 152

                          90
                  ....*....|....
gi 1633648422 250 AE--VRQKKPVNGV 261
Cdd:PRK02854  153 ASngGQPKRDINTV 166
DnaT pfam17948
DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain ...
 187-259 1.87e-16

DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in Swiss:P0A8J2 can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N- and C- terminals are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to pfam08585 except that it contains an extra loop at the N-terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilization of the three-helix bundle.


Pssm-ID: 465580  Cd Length: 69  Bit Score: 72.67  E-value: 1.87e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1633648422 187 FAMYFGWKPSEDFPRLATIWGMPLRPGINlaAELSSFIAYWQAEGraFHQVQWEQKLARHLNRAEVRQKKPVN 259
Cdd:pfam17948   1 FPMHLDWQPSADFLEILALAGGIDRDFAE--DELPEFVLYWRERG--FAQHQWNQKFVQHVKRQWARYQSSLG 69
ECs1768 COG5529
Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: ...
 199-269 1.66e-07

Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: prophages, transposons];


Pssm-ID: 444280  Cd Length: 104  Bit Score: 48.72  E-value: 1.66e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1633648422 199 FPRLATIWGMPLrpginlaAELSSFIAYWQAEGRAFHQvqwEQKLARHLNRAE-VRQKKPVNGVNDHVGVRA 269
Cdd:COG5529     1 FSRQAALWGIAL-------PELAAFRAHWQKHGKEFGS---QQKLARYVQQARaFVNRPPRRDRGTLTKTRP 62
HTH_36 pfam13730
Helix-turn-helix domain;
11-62 1.27e-06

Helix-turn-helix domain;


Pssm-ID: 463970 [Multi-domain]  Cd Length: 55  Bit Score: 44.79  E-value: 1.27e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1633648422  11 KSSAKAVLTWMADMCGADLCAFPSIPALAEATELDKKTVQSSLQYLVSIGLI 62
Cdd:pfam13730   4 SPTAKLLLLILASYANKDGGCFPSVETLAKRLGLSRRTIQRAIKELEELGYL 55
 
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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