Pseudomonas tremae strain PA-1-10F plasmid p2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Long read genomes of epiphytic Pseudomonas syringae from cherry orchards
Submitted (08-DEC-2020) Genetics, Genomics and Breeding, NIAB-EMR Genetics, Genomics and Breeding, New Road, East Malling, Kent ME19 6BJ, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nCP066272.1.\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 Date :: 01-DEC-2019\nAssembly Method :: Unicycler v. v0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 172x\nSequencing Technology :: Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/19/2023 04:43:57\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) :: 5,379\nCDSs (total) :: 5,296\nGenes (coding) :: 5,139\nCDSs (with protein) :: 5,139\nGenes (RNA) :: 83\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 63\nncRNAs :: 4\nPseudo Genes (total) :: 157\nCDSs (without protein) :: 157\nPseudo Genes (ambiguous residues) :: 0 of 157\nPseudo Genes (frameshifted) :: 65 of 157\nPseudo Genes (incomplete) :: 101 of 157\nPseudo Genes (internal stop) :: 36 of 157\nPseudo Genes (multiple problems) :: 37 of 157\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_003373511.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004667013.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015649575.1
COORDINATES: similar to AA sequence:RefSeq:WP_015649574.1
COORDINATES: similar to AA sequence:RefSeq:WP_005524330.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558319.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
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_004661238.1
COORDINATES: similar to AA sequence:RefSeq:WP_004661241.1
COORDINATES: protein motif:HMM:NF024830.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_005730279.1
COORDINATES: similar to AA sequence:RefSeq:WP_005730278.1
COORDINATES: similar to AA sequence:RefSeq:WP_020304372.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004667962.1
COORDINATES: similar to AA sequence:RefSeq:WP_003381808.1
COORDINATES: similar to AA sequence:RefSeq:WP_004662083.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004667960.1
frameshifted; 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_004661061.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668066.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668036.1
COORDINATES: similar to AA sequence:RefSeq:WP_004407087.1
COORDINATES: similar to AA sequence:RefSeq:WP_007247495.1
type VI secretion system tube protein Hcp
COORDINATES: similar to AA sequence:RefSeq:WP_015873600.1
COORDINATES: similar to AA sequence:RefSeq:WP_000007431.1
COORDINATES: similar to AA sequence:RefSeq:WP_005747127.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556034.1
COORDINATES: similar to AA sequence:RefSeq:WP_005769720.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666908.1
COORDINATES: similar to AA sequence:RefSeq:WP_017684526.1
COORDINATES: similar to AA sequence:RefSeq:WP_005622131.1
COORDINATES: similar to AA sequence:RefSeq:WP_020304521.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010209223.1
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_002556075.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:NP_490533.1
COORDINATES: similar to AA sequence:RefSeq:WP_011103324.1
GO:0030254 - protein secretion by the type III secretion system [Evidence IEA]
XopB/HopD1 family type III secretion system effector
COORDINATES: similar to AA sequence:RefSeq:WP_003381763.1
COORDINATES: similar to AA sequence:RefSeq:WP_003414764.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667176.1
COORDINATES: similar to AA sequence:RefSeq:WP_010207371.1
Com family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011107020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011107021.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005740405.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011107023.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003344336.1
COORDINATES: similar to AA sequence:RefSeq:WP_003344338.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004668202.1
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005622143.1
COORDINATES: similar to AA sequence:RefSeq:WP_005740400.1
lytic transglycosylase domain-containing 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_020325434.1
type IV secretion system DotC family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005759128.1
COORDINATES: similar to AA sequence:RefSeq:WP_004643879.1
COORDINATES: similar to AA sequence:RefSeq:WP_007247250.1
COORDINATES: similar to AA sequence:RefSeq:WP_010208376.1
COORDINATES: similar to AA sequence:RefSeq:WP_003344363.1
COORDINATES: similar to AA sequence:RefSeq:WP_007247249.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331471.1
COORDINATES: similar to AA sequence:RefSeq:WP_004661192.1
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_005622162.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_010209698.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331473.1
COORDINATES: similar to AA sequence:RefSeq:WP_020325426.1
COORDINATES: similar to AA sequence:RefSeq:WP_005759143.1
COORDINATES: similar to AA sequence:RefSeq:WP_010209692.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556014.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556016.1
COORDINATES: similar to AA sequence:RefSeq:WP_003344384.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666879.1
COORDINATES: similar to AA sequence:RefSeq:WP_003344389.1
COORDINATES: similar to AA sequence:RefSeq:WP_005759157.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_007247236.1
COORDINATES: similar to AA sequence:RefSeq:WP_004644068.1
COORDINATES: similar to AA sequence:RefSeq:WP_011106997.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005769748.1
thioredoxin fold domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020325419.1
F-type conjugative transfer protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_003381788.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]