Pseudomonas tremae strain PA-1-10F plasmid p1, 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\nCP066271.1.\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_002556085.1
COORDINATES: similar to AA sequence:RefSeq:WP_007915612.1
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_076612095.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003436862.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569390.1
COORDINATES: similar to AA sequence:RefSeq:WP_017279394.1
COORDINATES: similar to AA sequence:RefSeq:WP_020304503.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569388.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569387.1
COORDINATES: similar to AA sequence:RefSeq:WP_011103214.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003349456.1
type III secretion system YopJ family effector HopZ2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019332287.1
COORDINATES: similar to AA sequence:RefSeq:WP_005771833.1
COORDINATES: similar to AA sequence:RefSeq:WP_001262004.1
COORDINATES: similar to AA sequence:RefSeq:WP_011282515.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331447.1
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_011103208.1
GO:0070403 - NAD+ binding [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Sir2 family NAD-dependent protein deacetylase
COORDINATES: protein motif:HMM:NF041728.1
COORDINATES: similar to AA sequence:RefSeq:WP_005734906.1
COORDINATES: similar to AA sequence:RefSeq:WP_017699228.1
COORDINATES: similar to AA sequence:RefSeq:WP_005772647.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003117291.1
COORDINATES: similar to AA sequence:RefSeq:WP_004663854.1
frameshifted; 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:WP_011167363.1
IS21-like element ISPsy20 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_013104226.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005888835.1
coronamic acid biosynthesis protein CmaL
COORDINATES: similar to AA sequence:RefSeq:WP_003410995.1
COORDINATES: similar to AA sequence:RefSeq:WP_032489554.1
COORDINATES: similar to AA sequence:RefSeq:WP_007252515.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020307977.1
GO:0000036 - acyl carrier activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004666806.1
COORDINATES: similar to AA sequence:RefSeq:WP_010207026.1
GO:0004315 - 3-oxoacyl-[acyl-carrier-protein] synthase activity [Evidence IEA]
beta-ketoacyl-[acyl-carrier-protein] synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004666808.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666809.1
COORDINATES: similar to AA sequence:RefSeq:WP_020307975.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666811.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666812.1
GO:0047617 - acyl-CoA hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010207037.1
GO:0043880 - crotonyl-CoA reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004666814.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
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_010208439.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020309191.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_004666820.1
COORDINATES: similar to AA sequence:RefSeq:WP_005734270.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666822.1
L-allo-isoleucine:holo-[CmaA peptidyl-carrier protein] ligase
COORDINATES: similar to AA sequence:RefSeq:WP_004666823.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666824.1
COORDINATES: similar to AA sequence:RefSeq:WP_007251966.1
COORDINATES: similar to AA sequence:RefSeq:WP_010562554.1
COORDINATES: similar to AA sequence:RefSeq:WP_005888844.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611532.1
COORDINATES: similar to AA sequence:RefSeq:WP_003316225.1
COORDINATES: similar to AA sequence:RefSeq:WP_020304266.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005746122.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_002556077.1
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_004663932.1
COORDINATES: similar to AA sequence:RefSeq:WP_011169510.1
IS630-like element ISPsy25 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_017700514.1
GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017700513.1
COORDINATES: similar to AA sequence:RefSeq:WP_020318227.1
COORDINATES: similar to AA sequence:RefSeq:WP_017700511.1
COORDINATES: protein motif:HMM:NF027964.2
saccharopine dehydrogenase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF015400.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
saccharopine dehydrogenase NADP-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003381412.1
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_005783225.1
COORDINATES: similar to AA sequence:RefSeq:WP_003436798.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019648569.1
polyamine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003319387.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668202.1
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016569404.1
COORDINATES: similar to AA sequence:RefSeq:WP_003407112.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019334638.1
COORDINATES: similar to AA sequence:RefSeq:WP_011282553.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_003407107.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667061.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017279425.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667984.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569412.1
COORDINATES: similar to AA sequence:RefSeq:WP_003117273.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220837.1
COORDINATES: similar to AA sequence:RefSeq:WP_003179778.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003382250.1
COORDINATES: protein motif:HMM:NF041292.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569425.1
COORDINATES: similar to AA sequence:RefSeq:WP_005782542.1
COORDINATES: similar to AA sequence:RefSeq:WP_010217615.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010217604.1
COORDINATES: similar to AA sequence:RefSeq:WP_005782535.1
COORDINATES: similar to AA sequence:RefSeq:WP_003407061.1