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Conserved domains on  [gi|2525667178|ref|WP_287451544|]
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DNA-processing protein DprA, partial [Brochothrix sp.]

Protein Classification

LOG family protein( domain architecture ID 366823)

LOG (Lonely Guy) family protein may function as a hydrolase, similar to Arabidopsis thaliana cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG1 that converts inactive cytokinin nucleotides to the biologically active free-base forms

EC:  3.2.2.-
Gene Ontology:  GO:0016787
PubMed:  27507425|29901273

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Smf super family cl34034
Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake ...
 15-168 4.30e-67

Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0758:

Pssm-ID: 440521 [Multi-domain]  Cd Length: 360  Bit Score: 208.01  E-value: 4.30e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  15 IIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKELVISEYAPPISARKWTFV 94
Cdd:COG0758   133 LAAELAEAGFTVVSGLARGIDAAAHRGALEAGGKTIAVLGTGLDRIYPAEHRKLAERIAENGALVSEFPPGTPPLRGNFP 212

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2525667178  95 ERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVISADDILREI 168
Cdd:COG0758   213 RRNRIIAGLSLGVLVVEAAERSGSLITARLALEQGREVFAVPGSITSPRSAGCNRLIRQGAKLVTSAEDILEEL 286
 
Name Accession Description Interval E-value
Smf COG0758
Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake ...
 15-168 4.30e-67

Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake [Replication, recombination and repair];


Pssm-ID: 440521 [Multi-domain]  Cd Length: 360  Bit Score: 208.01  E-value: 4.30e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  15 IIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKELVISEYAPPISARKWTFV 94
Cdd:COG0758   133 LAAELAEAGFTVVSGLARGIDAAAHRGALEAGGKTIAVLGTGLDRIYPAEHRKLAERIAENGALVSEFPPGTPPLRGNFP 212

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2525667178  95 ERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVISADDILREI 168
Cdd:COG0758   213 RRNRIIAGLSLGVLVVEAAERSGSLITARLALEQGREVFAVPGSITSPRSAGCNRLIRQGAKLVTSAEDILEEL 286
DNA_processg_A pfam02481
DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a ...
 1-160 1.28e-60

DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyze the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation.


Pssm-ID: 426793  Cd Length: 210  Bit Score: 186.59  E-value: 1.28e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178   1 ARQCNKGIDRVMQPIIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKE-LVI 79
Cdd:pfam02481  50 TRKASAYGKRVARKLAAELAEAGITIVSGLARGIDAAAHRAALEAGGRTIAVLGTGLDIIYPRENRKLAERIAEQGgLLL 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  80 SEYAPPISARKWTFVERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVI 159
Cdd:pfam02481 130 SEYPPGTPPLRYHFPKRNRIIAGLSRATLVVEAALKSGALITARLALEQGREVFAVPGPIFSPLSKGCNRLIKEGAKLVT 209


                  .
gi 2525667178 160 S 160
Cdd:pfam02481 210 S 210
dprA TIGR00732
DNA protecting protein DprA; Disruption of this gene in both Haemophilus influenzae and ...
 2-167 1.97e-51

DNA protecting protein DprA; Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function. [Cellular processes, DNA transformation]


Pssm-ID: 273238  Cd Length: 220  Bit Score: 163.65  E-value: 1.97e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178   2 RQCNKGIDRVMQPIIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRK-ELVIS 80
Cdd:TIGR00732  53 RRPTKYGERWTRKLAEELAKNGVTIVSGLALGIDGIAHKAALKVNGRTIAVLGTGLDQIYPRQNSKLAAKIAENgGLLLS 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  81 EYAPPISARKWTFVERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVIS 160
Cdd:TIGR00732 133 EYPPDTKPIKYNFPKRNRIISGLSRAVLVVEAPLKSGALITARYALEQGREVFAYPGDLNSPESDGCHKLIEQGAALITS 212


                  ....*..
gi 2525667178 161 ADDILRE 167
Cdd:TIGR00732 213 AKDILET 219
PRK10736 PRK10736
DNA-protecting protein DprA;
18-168 3.18e-38

DNA-protecting protein DprA;


Pssm-ID: 236747 [Multi-domain]  Cd Length: 374  Bit Score: 133.92  E-value: 3.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  18 QLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKE-LVISEY---APPISARkwtF 93
Cdd:PRK10736  132 ELAKNGLTITSGLARGIDGVAHRAALQAGGKTIAVLGNGLENIYPRRHARLAESIIEQGgALVSEFpldTPPLAAN---F 208

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2525667178  94 VERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVISADDILREI 168
Cdd:PRK10736  209 PRRNRIISGLSKGVLVVEAALRSGSLVTARCALEQGRDVFALPGPIGNPGSEGPHWLIKQGAYLVTSPEDILENL 283
 
Name Accession Description Interval E-value
Smf COG0758
Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake ...
 15-168 4.30e-67

Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake [Replication, recombination and repair];


Pssm-ID: 440521 [Multi-domain]  Cd Length: 360  Bit Score: 208.01  E-value: 4.30e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  15 IIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKELVISEYAPPISARKWTFV 94
Cdd:COG0758   133 LAAELAEAGFTVVSGLARGIDAAAHRGALEAGGKTIAVLGTGLDRIYPAEHRKLAERIAENGALVSEFPPGTPPLRGNFP 212

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2525667178  95 ERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVISADDILREI 168
Cdd:COG0758   213 RRNRIIAGLSLGVLVVEAAERSGSLITARLALEQGREVFAVPGSITSPRSAGCNRLIRQGAKLVTSAEDILEEL 286
DNA_processg_A pfam02481
DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a ...
 1-160 1.28e-60

DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyze the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation.


Pssm-ID: 426793  Cd Length: 210  Bit Score: 186.59  E-value: 1.28e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178   1 ARQCNKGIDRVMQPIIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKE-LVI 79
Cdd:pfam02481  50 TRKASAYGKRVARKLAAELAEAGITIVSGLARGIDAAAHRAALEAGGRTIAVLGTGLDIIYPRENRKLAERIAEQGgLLL 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  80 SEYAPPISARKWTFVERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVI 159
Cdd:pfam02481 130 SEYPPGTPPLRYHFPKRNRIIAGLSRATLVVEAALKSGALITARLALEQGREVFAVPGPIFSPLSKGCNRLIKEGAKLVT 209


                  .
gi 2525667178 160 S 160
Cdd:pfam02481 210 S 210
dprA TIGR00732
DNA protecting protein DprA; Disruption of this gene in both Haemophilus influenzae and ...
 2-167 1.97e-51

DNA protecting protein DprA; Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function. [Cellular processes, DNA transformation]


Pssm-ID: 273238  Cd Length: 220  Bit Score: 163.65  E-value: 1.97e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178   2 RQCNKGIDRVMQPIIKQLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRK-ELVIS 80
Cdd:TIGR00732  53 RRPTKYGERWTRKLAEELAKNGVTIVSGLALGIDGIAHKAALKVNGRTIAVLGTGLDQIYPRQNSKLAAKIAENgGLLLS 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  81 EYAPPISARKWTFVERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVIS 160
Cdd:TIGR00732 133 EYPPDTKPIKYNFPKRNRIISGLSRAVLVVEAPLKSGALITARYALEQGREVFAYPGDLNSPESDGCHKLIEQGAALITS 212


                  ....*..
gi 2525667178 161 ADDILRE 167
Cdd:TIGR00732 213 AKDILET 219
PRK10736 PRK10736
DNA-protecting protein DprA;
18-168 3.18e-38

DNA-protecting protein DprA;


Pssm-ID: 236747 [Multi-domain]  Cd Length: 374  Bit Score: 133.92  E-value: 3.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2525667178  18 QLVIEDIGIVSGLATGIDTHAHRITLIEKGHTIAVLGSGMYRLYPQENALLYNYMLRKE-LVISEY---APPISARkwtF 93
Cdd:PRK10736  132 ELAKNGLTITSGLARGIDGVAHRAALQAGGKTIAVLGNGLENIYPRRHARLAESIIEQGgALVSEFpldTPPLAAN---F 208

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2525667178  94 VERNRLVSALSQGVWVVEAAEKSGSLITVDYALDEGKSIFATPGSPLNKQAVGCNRLLQEGAILVISADDILREI 168
Cdd:PRK10736  209 PRRNRIISGLSKGVLVVEAALRSGSLVTARCALEQGRDVFALPGPIGNPGSEGPHWLIKQGAYLVTSPEDILENL 283
 
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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