Pseudomonas siliginis strain OTU6BANIB1 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacterial species interacting with Arabidopsis thaliana in natural habitats
Submitted (13-JUN-2022) SPE, INRAE, UMR1349 IGEPP INRA BP35327, Le Rheu 35653, France
REFSEQ INFORMATION: The reference sequence is identical to\nCP099597.1.\nBacteria and source DNA available from Fabrice Roux, LIPME\nINRAE-CNRS, 24 Chemin de Borde Rouge - Auzeville CS 52627 31326\nCastanet Tolosan cedex, France.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: FLYE v. 2.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 54.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/08/2023 03:59:07\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,515\nCDSs (total) :: 5,427\nGenes (coding) :: 5,388\nCDSs (with protein) :: 5,388\nGenes (RNA) :: 88\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 68\nncRNAs :: 4\nPseudo Genes (total) :: 39\nCDSs (without protein) :: 39\nPseudo Genes (ambiguous residues) :: 0 of 39\nPseudo Genes (frameshifted) :: 7 of 39\nPseudo Genes (incomplete) :: 33 of 39\nPseudo Genes (internal stop) :: 5 of 39\nPseudo Genes (multiple problems) :: 6 of 39\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011875929.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF016785.2
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_006682550.1
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:TIGR03021.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:TIGR02520.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007183072.1
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins.; Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007183073.1
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_017891124.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_004666790.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344230.1
COORDINATES: similar to AA sequence:RefSeq:WP_016359324.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005745047.1
GO:0003729 - mRNA binding [Evidence IEA]
type II toxin-antitoxin system HicA family toxin
COORDINATES: protein motif:HMM:TIGR02779.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020194526.1
COORDINATES: similar to AA sequence:RefSeq:WP_016359306.1
COORDINATES: similar to AA sequence:RefSeq:WP_016487000.1
COORDINATES: similar to AA sequence:RefSeq:WP_017849266.1
COORDINATES: similar to AA sequence:RefSeq:WP_005742387.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556034.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556111.1
adhesin biosynthesis transcription regulatory family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016359335.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005074609.1
COORDINATES: similar to AA sequence:RefSeq:WP_020795278.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666712.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_004666713.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183094.1
COORDINATES: similar to AA sequence:RefSeq:WP_004907748.1
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_007183098.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_011875709.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183101.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875706.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183103.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875703.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344329.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875700.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875690.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183065.1
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF019064.2
COORDINATES: similar to AA sequence:RefSeq:WP_003451619.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344220.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344218.1
COORDINATES: similar to AA sequence:RefSeq:WP_020192187.1
COORDINATES: similar to AA sequence:RefSeq:WP_016359372.1
COORDINATES: similar to AA sequence:RefSeq:WP_015026464.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875688.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008344165.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344177.1
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008344192.1
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_009682476.1
GO:0003896 - DNA primase activity [Evidence IEA]
GO:0006269 - DNA replication, synthesis of RNA primer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011875771.1
COORDINATES: similar to AA sequence:RefSeq:WP_017461408.1
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012403.2
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015272388.1
GO:0008168 - methyltransferase activity [Evidence IEA]