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The T4SS gene clusters in Ralstonia have variable gene organization and composition. Clusters are ordered based on their phylogenetic distribution: found only in RSSC phytopathogens, found in both or found only in non-RSSC environmentals. Genes in each cluster are labelled based on F/P/I/GI-type classification conventions: tra / trb (F-type), virB / D4 (P-type), an independent tra / trb scheme (I-type), and tfc (GI-type). The virB4 homologues have a bolded name ( traC , virB4 , traU , and tfc16 ) and a bolded gene arrow border. The genes annotated as the type IV coupling protein gene are labelled ‘CP’. ‘LT’ indicates genes annotated as lytic transglycosylase genes. Genes marked with an asterisk (*) are T4SS genes that were not able to be annotated within the indicated F/P/I/GI-type convention. Gene clusters were defined using Operon-mapper, MacSyFinder v2 with CONJscan models, <t>NCBI</t> RefSeq annotations, and NCBI Conserved Domain Database. Gene clusters were visualized with clinker and labelled with Affinity Designer. Gaps are displayed where the representative cluster had regions without predicted T4SS genes; patterns of non-T4SS genes are not always consistent among all members of each cluster. The representative cluster j is found on two separate contigs in the only Ralstonia genome with cluster j. For additional details regarding genome, gene, and protein NCBI accessions, see and Files S10–S26.
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The T4SS gene clusters in Ralstonia have variable gene organization and composition. Clusters are ordered based on their phylogenetic distribution: found only in RSSC phytopathogens, found in both or found only in non-RSSC environmentals. Genes in each cluster are labelled based on F/P/I/GI-type classification conventions: tra / trb (F-type), virB / D4 (P-type), an independent tra / trb scheme (I-type), and tfc (GI-type). The virB4 homologues have a bolded name ( traC , virB4 , traU , and tfc16 ) and a bolded gene arrow border. The genes annotated as the type IV coupling protein gene are labelled ‘CP’. ‘LT’ indicates genes annotated as lytic transglycosylase genes. Genes marked with an asterisk (*) are T4SS genes that were not able to be annotated within the indicated F/P/I/GI-type convention. Gene clusters were defined using Operon-mapper, MacSyFinder v2 with CONJscan models, NCBI RefSeq annotations, and NCBI Conserved Domain Database. Gene clusters were visualized with clinker and labelled with Affinity Designer. Gaps are displayed where the representative cluster had regions without predicted T4SS genes; patterns of non-T4SS genes are not always consistent among all members of each cluster. The representative cluster j is found on two separate contigs in the only Ralstonia genome with cluster j. For additional details regarding genome, gene, and protein NCBI accessions, see and Files S10–S26.

Journal: Microbial Genomics

Article Title: Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental Ralstonia

doi: 10.1099/mgen.0.001676

Figure Lengend Snippet: The T4SS gene clusters in Ralstonia have variable gene organization and composition. Clusters are ordered based on their phylogenetic distribution: found only in RSSC phytopathogens, found in both or found only in non-RSSC environmentals. Genes in each cluster are labelled based on F/P/I/GI-type classification conventions: tra / trb (F-type), virB / D4 (P-type), an independent tra / trb scheme (I-type), and tfc (GI-type). The virB4 homologues have a bolded name ( traC , virB4 , traU , and tfc16 ) and a bolded gene arrow border. The genes annotated as the type IV coupling protein gene are labelled ‘CP’. ‘LT’ indicates genes annotated as lytic transglycosylase genes. Genes marked with an asterisk (*) are T4SS genes that were not able to be annotated within the indicated F/P/I/GI-type convention. Gene clusters were defined using Operon-mapper, MacSyFinder v2 with CONJscan models, NCBI RefSeq annotations, and NCBI Conserved Domain Database. Gene clusters were visualized with clinker and labelled with Affinity Designer. Gaps are displayed where the representative cluster had regions without predicted T4SS genes; patterns of non-T4SS genes are not always consistent among all members of each cluster. The representative cluster j is found on two separate contigs in the only Ralstonia genome with cluster j. For additional details regarding genome, gene, and protein NCBI accessions, see and Files S10–S26.

Article Snippet: Bioinformatic analysis used sets of genomes: 394 RSSC phytopathogen genomes available as National Center for Biotechnology Information (NCBI) assemblies in 2023, 636 RSSC phytopathogen genomes available as NCBI assemblies or as raw reads on NCBI Sequence Read Archive (SRA) in 2024, 143 non-RSSC environmental genomes from 17 genomospecies available as NCBI assemblies in 2023, and 923 Burkholderiaceae family genomes that include the 394 RSSC phytopathogen genomes and 529 genomes from at least 252 genomospecies.

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