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Conserved domains on  [gi|16129320|ref|NP_415877|]
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DUF1376 domain-containing protein YdaU [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

YdaU family protein( domain architecture ID 10007954)

YdaU family protein is a DUF1376 domain-containing protein; similar to Escherichia coli protein YdaU

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YdaU COG3756
Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown];
19-134 1.16e-44

Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown];


:

Pssm-ID: 442970  Cd Length: 124  Bit Score: 147.45  E-value: 1.16e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129320  19 AALPYMQLYIADYLADTMHLSAEEHGAYLLLMFNYWQTGKPIPKN--RLA-KIARLTNERWADVEPSLQEFFCDNGEEWV 95
Cdd:COG3756   1 SAMPYYPLYIGDYLADTRHLSAEEHGIYLLLLDAYWARGGPLPDDdaRLArLIGARSPEEWAAVEAVLAEFFELRDGGWR 80

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 16129320  96 HLRIEEDLASVREKLTKKSAAGKASVQARRSRKEADVQT 134
Cdd:COG3756  81 NHRLEEEIAKARAKAEKRSEAGRKGARKRQKKKEADRQS 119
DnaT super family cl46275
DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain ...
 267-285 5.01e-03

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: 37.09  E-value: 5.01e-03
                         10
                 ....*....|....*....
gi 16129320  267 RQVNTVSLPDSAIPPGFRG 285
Cdd:PRK02854 161 RDINTVSEPDSQIPPGFRG 179
 
Name Accession Description Interval E-value
YdaU COG3756
Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown];
19-134 1.16e-44

Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown];


Pssm-ID: 442970  Cd Length: 124  Bit Score: 147.45  E-value: 1.16e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129320  19 AALPYMQLYIADYLADTMHLSAEEHGAYLLLMFNYWQTGKPIPKN--RLA-KIARLTNERWADVEPSLQEFFCDNGEEWV 95
Cdd:COG3756   1 SAMPYYPLYIGDYLADTRHLSAEEHGIYLLLLDAYWARGGPLPDDdaRLArLIGARSPEEWAAVEAVLAEFFELRDGGWR 80

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 16129320  96 HLRIEEDLASVREKLTKKSAAGKASVQARRSRKEADVQT 134
Cdd:COG3756  81 NHRLEEEIAKARAKAEKRSEAGRKGARKRQKKKEADRQS 119
DUF1376 pfam07120
Protein of unknown function (DUF1376); This family consists of several hypothetical bacterial ...
 22-101 1.70e-29

Protein of unknown function (DUF1376); This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.


Pssm-ID: 462094  Cd Length: 83  Bit Score: 106.94  E-value: 1.70e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129320    22 PYMQLYIADYLADTMHLSAEEHGAYLLLMFNYWQTGKPIP--KNRLAKIARLTNERW-ADVEPSLQEFF--CDNGeeWVH 96
Cdd:pfam07120   1 NYYPHHIGDYARDTAHLSALEHGAYRLLLDLYYDTEGPIPddDRRLARLCGARTEEWrAAVEFVLAEFFdlQDGG--WHN 78


                  ....*
gi 16129320    97 LRIEE 101
Cdd:pfam07120  79 ARCEE 83
PRK02854 PRK02854
primosomal protein DnaT;
267-285 5.01e-03

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 37.09  E-value: 5.01e-03
                         10
                 ....*....|....*....
gi 16129320  267 RQVNTVSLPDSAIPPGFRG 285
Cdd:PRK02854 161 RDINTVSEPDSQIPPGFRG 179
 
Name Accession Description Interval E-value
YdaU COG3756
Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown];
19-134 1.16e-44

Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown];


Pssm-ID: 442970  Cd Length: 124  Bit Score: 147.45  E-value: 1.16e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129320  19 AALPYMQLYIADYLADTMHLSAEEHGAYLLLMFNYWQTGKPIPKN--RLA-KIARLTNERWADVEPSLQEFFCDNGEEWV 95
Cdd:COG3756   1 SAMPYYPLYIGDYLADTRHLSAEEHGIYLLLLDAYWARGGPLPDDdaRLArLIGARSPEEWAAVEAVLAEFFELRDGGWR 80

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 16129320  96 HLRIEEDLASVREKLTKKSAAGKASVQARRSRKEADVQT 134
Cdd:COG3756  81 NHRLEEEIAKARAKAEKRSEAGRKGARKRQKKKEADRQS 119
DUF1376 pfam07120
Protein of unknown function (DUF1376); This family consists of several hypothetical bacterial ...
 22-101 1.70e-29

Protein of unknown function (DUF1376); This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.


Pssm-ID: 462094  Cd Length: 83  Bit Score: 106.94  E-value: 1.70e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129320    22 PYMQLYIADYLADTMHLSAEEHGAYLLLMFNYWQTGKPIP--KNRLAKIARLTNERW-ADVEPSLQEFF--CDNGeeWVH 96
Cdd:pfam07120   1 NYYPHHIGDYARDTAHLSALEHGAYRLLLDLYYDTEGPIPddDRRLARLCGARTEEWrAAVEFVLAEFFdlQDGG--WHN 78


                  ....*
gi 16129320    97 LRIEE 101
Cdd:pfam07120  79 ARCEE 83
PRK02854 PRK02854
primosomal protein DnaT;
267-285 5.01e-03

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 37.09  E-value: 5.01e-03
                         10
                 ....*....|....*....
gi 16129320  267 RQVNTVSLPDSAIPPGFRG 285
Cdd:PRK02854 161 RDINTVSEPDSQIPPGFRG 179
 
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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