Pseudomonas ficuserectae strain ZJDX-003 plasmid pZJDX1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Genome Sequencing of Pseudomonas syringae strain ZJDX-003
Submitted (22-OCT-2021) Department of Sericulture, South china agriculture university, Wushan, Guangzhou, Guangdong 510642, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP085685.1.\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 Method :: Canu v. 1.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 366.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 08/08/2022 13:05:01\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 5,850\nCDSs (total) :: 5,766\nGenes (coding) :: 5,442\nCDSs (with protein) :: 5,442\nGenes (RNA) :: 84\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 64\nncRNAs :: 4\nPseudo Genes (total) :: 324\nCDSs (without protein) :: 324\nPseudo Genes (ambiguous residues) :: 0 of 324\nPseudo Genes (frameshifted) :: 124 of 324\nPseudo Genes (incomplete) :: 172 of 324\nPseudo Genes (internal stop) :: 84 of 324\nPseudo Genes (multiple problems) :: 50 of 324\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020303942.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024830.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558319.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005748813.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667960.1
COORDINATES: similar to AA sequence:RefSeq:WP_005734742.1
COORDINATES: similar to AA sequence:RefSeq:WP_014028961.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_013105051.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012477429.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611524.1
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_005782481.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004667035.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668202.1
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003319387.1
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_003436798.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331484.1
COORDINATES: similar to AA sequence:RefSeq:WP_007247495.1
type VI secretion system tube protein Hcp
COORDINATES: similar to AA sequence:RefSeq:WP_020358327.1
COORDINATES: similar to AA sequence:RefSeq:WP_005895504.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005740735.1
PBECR2 nuclease fold domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003436862.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666942.1
COORDINATES: similar to AA sequence:RefSeq:WP_020304499.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612095.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020304372.1
COORDINATES: similar to AA sequence:RefSeq:WP_005758211.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_076611465.1
IS3-like element IS51 family transposase
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_000198547.1
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_004667962.1
COORDINATES: similar to AA sequence:RefSeq:WP_003381808.1
COORDINATES: similar to AA sequence:RefSeq:WP_004662083.1
type II toxin-antitoxin system RelE/ParE family toxin
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004667013.1
COORDINATES: similar to AA sequence:RefSeq:WP_003519380.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565581.1
COORDINATES: similar to AA sequence:RefSeq:WP_011168094.1
XopAD/skwp family type III secretion system effector
COORDINATES: similar to AA sequence:RefSeq:WP_076612058.1
IS5-like element ISPsy2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011898609.1
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_017699228.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668036.1
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_019331440.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556002.1
COORDINATES: similar to AA sequence:RefSeq:WP_005747127.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666912.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666911.1
COORDINATES: similar to AA sequence:RefSeq:WP_016987647.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612240.1
COORDINATES: similar to AA sequence:RefSeq:WP_017699223.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077862.1
COORDINATES: similar to AA sequence:RefSeq:WP_005621995.1
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_018431613.1
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007175798.1
COORDINATES: similar to AA sequence:RefSeq:WP_004661993.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017157756.1
COORDINATES: similar to AA sequence:RefSeq:WP_019561439.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798593.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_014235306.1
COORDINATES: similar to AA sequence:RefSeq:WP_017847638.1
COORDINATES: similar to AA sequence:RefSeq:WP_003407112.1
COORDINATES: similar to AA sequence:RefSeq:WP_019334638.1
COORDINATES: similar to AA sequence:RefSeq:WP_016569407.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005782475.1
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_019331252.1
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_007253342.1
COORDINATES: similar to AA sequence:RefSeq:WP_017684942.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_017684943.1
frameshifted; 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_002556099.1
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010217141.1
COORDINATES: similar to AA sequence:RefSeq:WP_007253346.1
COORDINATES: similar to AA sequence:RefSeq:WP_004644125.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667069.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667999.1
COORDINATES: similar to AA sequence:RefSeq:WP_017684962.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003436834.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_016569421.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020304533.1
COORDINATES: similar to AA sequence:RefSeq:WP_017279381.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666800.1
COORDINATES: similar to AA sequence:RefSeq:WP_010217627.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666798.1
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_019331412.1
COORDINATES: similar to AA sequence:RefSeq:WP_005782535.1
COORDINATES: similar to AA sequence:RefSeq:WP_005730295.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003407061.1