Erwinia tracheiphila strain BHKY plasmid pETR004-b, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Erwinia.
Complete Genome Sequences of Four Strains of Erwinia tracheiphila, a bacterial plant pathogen with a highly complex genome
Submitted (16-DEC-2021) Plant Pathology and Microbiology, Iowa State University, 2213 Pammel Dr, Ames, IA 50011, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP089933.1.\nBacteria and source DNA available from Gwyn Beattie Lab, Iowa State\nUniversity, Department of Plant Pathology and Microbiology, 1344\nAdvanced Teaching & Research Bldg, 2213 Pammel Dr, Ames, IA, USA.\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 :: NOV-2021\nAssembly Method :: Flye v. 2.9; Raven v. 1.6.1; Unicycler v.\n 0.4.9; Miniasm v. 0.3; Minipolish v.\n 0.1.3; NextDenovo v. 2.5.0; NextPolish v.\n 1.4.0; Trycycler v. 0.4.1; Racon v.\n 1.6.1; Medaka v. 1.4.1; SMRTLink Arrow v.\n 7.0.1; Circlator v. 1.5.5\nAssembly Name :: BHKY_assembly_2021\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 71.0x\nSequencing Technology :: Oxford Nanopore MinION; PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/08/2022 10:01:55\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,143\nCDSs (total) :: 5,054\nGenes (coding) :: 4,223\nCDSs (with protein) :: 4,223\nGenes (RNA) :: 89\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 65\nncRNAs :: 5\nPseudo Genes (total) :: 831\nCDSs (without protein) :: 831\nPseudo Genes (ambiguous residues) :: 0 of 831\nPseudo Genes (frameshifted) :: 465 of 831\nPseudo Genes (incomplete) :: 474 of 831\nPseudo Genes (internal stop) :: 290 of 831\nPseudo Genes (multiple problems) :: 339 of 831\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_002225475.1
GO:0006276 - plasmid maintenance [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
incFII family plasmid replication initiator RepA
COORDINATES: similar to AA sequence:RefSeq:WP_012592917.1
COORDINATES: protein motif:HMM:NF013561.2
COORDINATES: similar to AA sequence:RefSeq:WP_004144477.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_000510385.1
COORDINATES: similar to AA sequence:RefSeq:WP_001361845.1
COORDINATES: similar to AA sequence:RefSeq:WP_014543172.1
COORDINATES: similar to AA sequence:RefSeq:WP_016192563.1
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004937746.1
COORDINATES: similar to AA sequence:RefSeq:WP_032495017.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549893.1
COORDINATES: similar to AA sequence:RefSeq:WP_004026069.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_000127484.1
COORDINATES: similar to AA sequence:RefSeq:NP_490535.1
COORDINATES: similar to AA sequence:RefSeq:NP_490534.1
COORDINATES: similar to AA sequence:RefSeq:NP_490533.1
COORDINATES: similar to AA sequence:RefSeq:WP_020322723.1
COORDINATES: similar to AA sequence:RefSeq:WP_006122357.1
COORDINATES: protein motif:HMM:NF017105.2
COORDINATES: similar to AA sequence:RefSeq:WP_000343613.1
COORDINATES: similar to AA sequence:RefSeq:WP_004131847.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001568075.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF024991.2
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [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.
COORDINATES: protein motif:HMM:NF018726.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_016193191.1
COORDINATES: similar to AA sequence:RefSeq:WP_008324931.1
COORDINATES: similar to AA sequence:RefSeq:WP_001485405.1