Pectobacterium parmentieri strain IFB5427 plasmid pPAR01, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Pectobacteriaceae; Pectobacterium.
High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes
Submitted (27-FEB-2018) Department of Biotechnology, University of Gdansk, Intercollegiate Faculty of Biotechnology UG&MUG, Abrahama 58, Gdansk 30-307, Poland
REFSEQ INFORMATION: The reference sequence is identical to\nCP027261.1.\nBacteria and source DNA available from Intercollegiate Faculty of\nBiotechnology of University of Gdansk and Medical University of\nGdansk, Gdansk, Poland.\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 :: 04-MAY-2016\nAssembly Method :: SPAdes v. JUNE-2016\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 75.0x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 13:48:12\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) :: 4,885\nCDSs (total) :: 4,779\nGenes (coding) :: 4,685\nCDSs (with protein) :: 4,685\nGenes (RNA) :: 106\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 76\nncRNAs :: 8\nPseudo Genes (total) :: 94\nCDSs (without protein) :: 94\nPseudo Genes (ambiguous residues) :: 0 of 94\nPseudo Genes (frameshifted) :: 31 of 94\nPseudo Genes (incomplete) :: 73 of 94\nPseudo Genes (internal stop) :: 20 of 94\nPseudo Genes (multiple problems) :: 27 of 94\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013632.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017374633.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_011092164.1
COORDINATES: similar to AA sequence:RefSeq:WP_004720812.1
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_017374630.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004720814.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374628.1
COORDINATES: protein motif:HMM:NF039512.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: similar to AA sequence:RefSeq:WP_017374635.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_017891014.1
COORDINATES: similar to AA sequence:RefSeq:WP_004720818.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374625.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_004720823.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374622.1
COORDINATES: similar to AA sequence:RefSeq:WP_004720828.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374619.1
COORDINATES: similar to AA sequence:RefSeq:WP_004720831.1
COORDINATES: protein motif:HMM:NF033887.1
COORDINATES: similar to AA sequence:RefSeq:WP_004720832.1
COORDINATES: similar to AA sequence:RefSeq:WP_001595120.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_020317119.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF033891.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_004720838.1
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_004720841.1
F-type conjugative transfer protein TrbC
COORDINATES: protein motif:HMM:NF015397.2
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_004720848.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000130127.1
molybdopterin-guanine dinucleotide biosynthesis protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_000113358.1
COORDINATES: protein motif:HMM:NF039307.1
COORDINATES: similar to AA sequence:RefSeq:WP_004131751.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF027824.2
COORDINATES: similar to AA sequence:RefSeq:WP_019584489.1
COORDINATES: similar to AA sequence:RefSeq:WP_015841322.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843197.1
COORDINATES: protein motif:HMM:NF018636.2
COORDINATES: protein motif:HMM:NF018044.2
conjugation system SOS inhibitor PsiB family protein
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_004940313.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087183.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF018792.2
COORDINATES: protein motif:HMM:NF015205.2
COORDINATES: similar to AA sequence:RefSeq:WP_013087144.1
COORDINATES: similar to AA sequence:RefSeq:NP_052645.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322837.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004146678.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152715.1
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_000030202.1
COORDINATES: similar to AA sequence:RefSeq:WP_012908943.1
COORDINATES: similar to AA sequence:RefSeq:WP_000074442.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_000983043.1
COORDINATES: similar to AA sequence:RefSeq:WP_017694190.1
COORDINATES: similar to AA sequence:RefSeq:WP_017694189.1
COORDINATES: similar to AA sequence:RefSeq:WP_010308663.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013811197.1
COORDINATES: similar to AA sequence:RefSeq:WP_001297030.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229629.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:YP_005229630.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008786839.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001523436.1
COORDINATES: similar to AA sequence:RefSeq:WP_007372294.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322659.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_006122473.1
GO:0006276 - plasmid maintenance [Evidence IEA]
incFII family plasmid replication initiator RepA
COORDINATES: protein motif:HMM:NF014417.2
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000426471.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF022136.2
COORDINATES: protein motif:HMM:NF019064.2
COORDINATES: similar to AA sequence:RefSeq:WP_000984842.1
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:NF018562.2
COORDINATES: protein motif:HMM:TIGR03021.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017374638.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374637.1
COORDINATES: similar to AA sequence:RefSeq:WP_017374636.1