DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a ...
119-323
1.63e-71
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: 223.95 E-value: 1.63e-71
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
391-428
9.05e-04
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
The actual alignment was detected with superfamily member cd00092:
Pssm-ID: 481199 [Multi-domain] Cd Length: 67 Bit Score: 37.65 E-value: 9.05e-04
DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a ...
119-323
1.63e-71
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: 223.95 E-value: 1.63e-71
DNA protecting protein DprA; Disruption of this gene in both Haemophilus influenzae and ...
121-327
3.13e-25
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: 102.79 E-value: 3.13e-25
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
391-428
9.05e-04
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Pssm-ID: 238044 [Multi-domain] Cd Length: 67 Bit Score: 37.65 E-value: 9.05e-04
DNA recombination-mediator protein A; The SMF family, of DNA processing chain A, dprA, are a ...
119-323
1.63e-71
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: 223.95 E-value: 1.63e-71
DNA protecting protein DprA; Disruption of this gene in both Haemophilus influenzae and ...
121-327
3.13e-25
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: 102.79 E-value: 3.13e-25
SLOG cluster4 family; Family in the SLOG superfamily, observed as a standalone domain with ...
166-222
3.30e-06
SLOG cluster4 family; Family in the SLOG superfamily, observed as a standalone domain with little informative genome context, although related families in the SLOG superfamily are predicted to function in diverse conflict contexts.
Pssm-ID: 436397 Cd Length: 152 Bit Score: 46.81 E-value: 3.30e-06
TIGR00725 family protein; This model represents one branch of a subfamily of uncharacterized ...
165-295
6.13e-06
TIGR00725 family protein; This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE. [Hypothetical proteins, Conserved]
Pssm-ID: 129808 Cd Length: 159 Bit Score: 46.00 E-value: 6.13e-06
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
391-428
9.05e-04
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Pssm-ID: 238044 [Multi-domain] Cd Length: 67 Bit Score: 37.65 E-value: 9.05e-04
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
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Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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