Pseudomonas lurida strain L228 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Draft Genome Sequence of Three Endophyte Strains of Pseudomonas fluorescens isolated from Miscanthus giganteus
Submitted (09-MAY-2016) Envirocore, Dargan Research Centre, Institute of Technology Carlow, Kilkenny Road, Carlow, Carlow R93 V960, Ireland
REFSEQ INFORMATION: The reference sequence is identical to\nCP015640.1.\nSource bacteria available from Envirocore, The Dargan Research\nCentre, Institute of Technology, Carlow, Kilkenny Road, Carlow.\nRepublic of Ireland.\nThe organism was changed from 'Pseudomonas fluorescens' to\n'Pseudomonas lurida' in July 2019.\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##Taxonomic-Update-Statistics-START##\nThis Genome (query) :: GCA_001708485.1\nCurrent Name :: Pseudomonas lurida\nPrevious Name :: Pseudomonas fluorescens\nDate Updated :: 2019-07-29\nAnalysis Type :: Average Nucleotide Identity (ANI)\nAnalysis 1 (A1) :: Query vs. TYPE genome for current name\nA1 Genome (subject) :: GCA_002563895.1\nA1 Name :: Pseudomonas lurida\nA1 ANI :: 99.27%\nA1 Query Coverage :: 91.04%\nA1 Subject Coverage :: 90.2%\nAnalysis 2 (A2) :: Query vs. TYPE genome for previous name\nA2 Genome (subject) :: GCA_003417575.1\nA2 Name :: Pseudomonas fluorescens\nA2 ANI :: 87.87%\nA2 Query Coverage :: 73.26%\nA2 Subject Coverage :: 71.05%\n##Taxonomic-Update-Statistics-END##\n\n##Genome-Assembly-Data-START##\nAssembly Method :: SPAdes v. 2.4\nGenome Coverage :: missing\nSequencing Technology :: Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 00:41:32\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,783\nCDSs (total) :: 5,711\nGenes (coding) :: 5,627\nCDSs (with protein) :: 5,627\nGenes (RNA) :: 72\nrRNAs :: 1, 5, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 5, 1 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 4\nPseudo Genes (total) :: 84\nCDSs (without protein) :: 84\nPseudo Genes (ambiguous residues) :: 0 of 84\nPseudo Genes (frameshifted) :: 27 of 84\nPseudo Genes (incomplete) :: 67 of 84\nPseudo Genes (internal stop) :: 13 of 84\nPseudo Genes (multiple problems) :: 19 of 84\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Interior of surface sterilised leaf tissue
COORDINATES: similar to AA sequence:RefSeq:WP_012439773.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017684526.1
COORDINATES: similar to AA sequence:RefSeq:WP_003149045.1
COORDINATES: similar to AA sequence:RefSeq:WP_010210211.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010213659.1
COORDINATES: similar to AA sequence:RefSeq:WP_017527425.1
COORDINATES: similar to AA sequence:RefSeq:WP_016359340.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666712.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009682528.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569388.1
COORDINATES: similar to AA sequence:RefSeq:WP_016359319.1
COORDINATES: similar to AA sequence:RefSeq:WP_003120987.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009045810.1
putative addiction module antidote protein
COORDINATES: similar to AA sequence:RefSeq:WP_016359365.1
COORDINATES: similar to AA sequence:RefSeq:WP_016359372.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020800409.1
COORDINATES: similar to AA sequence:RefSeq:WP_012229960.1
COORDINATES: similar to AA sequence:RefSeq:WP_004665467.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611532.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004299831.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007158801.1
COORDINATES: similar to AA sequence:RefSeq:WP_007955253.1
COORDINATES: similar to AA sequence:RefSeq:WP_017907170.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_019334953.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017709578.1
COORDINATES: similar to AA sequence:RefSeq:WP_017709577.1
COORDINATES: similar to AA sequence:RefSeq:WP_004966285.1
F-type conjugative transfer protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_005759161.1
COORDINATES: similar to AA sequence:RefSeq:WP_011107038.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556019.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_015984373.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004666879.1
COORDINATES: similar to AA sequence:RefSeq:WP_004642775.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556016.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556014.1
COORDINATES: similar to AA sequence:RefSeq:WP_010218321.1
COORDINATES: similar to AA sequence:RefSeq:WP_020325426.1
COORDINATES: similar to AA sequence:RefSeq:WP_011107032.1
COORDINATES: similar to AA sequence:RefSeq:WP_010209698.1
COORDINATES: similar to AA sequence:RefSeq:WP_005622162.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_013036413.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331471.1
COORDINATES: similar to AA sequence:RefSeq:WP_011107030.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036410.1
COORDINATES: similar to AA sequence:RefSeq:WP_005759128.1
COORDINATES: similar to AA sequence:RefSeq:WP_020325434.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011106980.1
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_005740400.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF013618.2
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_016359357.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:NF012485.2
COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016359370.1
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016359307.1
COORDINATES: similar to AA sequence:RefSeq:WP_003229994.1
COORDINATES: similar to AA sequence:RefSeq:WP_010209223.1
TraI/MobA(P) family conjugative relaxase