Duffyella gerundensis strain AR plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Duffyella.
Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions
Submitted (15-APR-2021) Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia
REFSEQ INFORMATION: The reference sequence is identical to\nCP073264.1.\nAnnotated using prokka 1.14.6 from\nhttps://github.com/tseemann/prokka.\nBacteria and source DNA available from AgriBio, 5 Ring Road,\nBundoora, Victoria 3083, Australia.\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 :: 31-MAR-2020\nAssembly Method :: Unicycler v. 0.4.8\nAssembly Name :: AVR_EgerAR_1.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/11/2023 01:57:16\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) :: 4,091\nCDSs (total) :: 3,984\nGenes (coding) :: 3,955\nCDSs (with protein) :: 3,955\nGenes (RNA) :: 107\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 8\nPseudo Genes (total) :: 29\nCDSs (without protein) :: 29\nPseudo Genes (ambiguous residues) :: 0 of 29\nPseudo Genes (frameshifted) :: 8 of 29\nPseudo Genes (incomplete) :: 20 of 29\nPseudo Genes (internal stop) :: 8 of 29\nPseudo Genes (multiple problems) :: 5 of 29\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008103203.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010246731.1
COORDINATES: similar to AA sequence:RefSeq:WP_010246735.1
COORDINATES: similar to AA sequence:RefSeq:WP_008924793.1
COORDINATES: similar to AA sequence:RefSeq:WP_003851702.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_012017296.1
COORDINATES: similar to AA sequence:RefSeq:WP_012017297.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199736.1
COORDINATES: similar to AA sequence:RefSeq:WP_010670294.1
COORDINATES: similar to AA sequence:RefSeq:WP_019082965.1
COORDINATES: similar to AA sequence:RefSeq:WP_007767577.1
COORDINATES: similar to AA sequence:RefSeq:WP_020456898.1
COORDINATES: similar to AA sequence:RefSeq:WP_011999000.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007885689.1
COORDINATES: similar to AA sequence:RefSeq:WP_013574303.1
COORDINATES: similar to AA sequence:RefSeq:WP_000879771.1
COORDINATES: similar to AA sequence:RefSeq:WP_000262326.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012968478.1
COORDINATES: similar to AA sequence:RefSeq:WP_017087772.1
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_013199757.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007885612.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199759.1
COORDINATES: similar to AA sequence:RefSeq:WP_004958593.1
TIGR03756 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_013199761.1
TIGR03757 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_007749362.1
COORDINATES: similar to AA sequence:RefSeq:WP_016151351.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014606052.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
glutaredoxin-dependent arsenate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_001549887.1
COORDINATES: similar to AA sequence:RefSeq:WP_007749371.1
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_007885632.1
COORDINATES: similar to AA sequence:RefSeq:WP_015056516.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004115530.1
TIGR03751 family conjugal transfer lipoprotein
COORDINATES: similar to AA sequence:RefSeq:WP_007885637.1
GO:0005886 - plasma membrane [Evidence IEA]
TIGR03752 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_013199767.1
TIGR03749 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_013199768.1
TIGR03746 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_013060273.1
TIGR03750 family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_015056511.1
TIGR03745 family integrating conjugative element membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_007885647.1
TIGR03758 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_016808261.1
RAQPRD family integrative conjugative element protein
COORDINATES: protein motif:HMM:NF020421.2
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
GO:0016070 - RNA metabolic process [Evidence IEA]
SymE family type I addiction module toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004716946.1
COORDINATES: similar to AA sequence:RefSeq:WP_019106674.1
COORDINATES: similar to AA sequence:RefSeq:WP_014593027.1
ShlB/FhaC/HecB family hemolysin secretion/activation protein
COORDINATES: similar to AA sequence:RefSeq:WP_016151314.1
TIGR03747 family integrating conjugative element membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_001510361.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_013199776.1
COORDINATES: similar to AA sequence:RefSeq:WP_013811166.1
COORDINATES: similar to AA sequence:RefSeq:WP_004181871.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016191739.1
TIGR03759 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_013811162.1
PilL N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012669271.1
COORDINATES: similar to AA sequence:RefSeq:WP_016807972.1
COORDINATES: similar to AA sequence:RefSeq:WP_007885441.1
COORDINATES: similar to AA sequence:RefSeq:WP_015056502.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199787.1
COORDINATES: similar to AA sequence:RefSeq:WP_001506264.1
TIGR03761 family integrating conjugative element protein
COORDINATES: similar to AA sequence:RefSeq:WP_010615558.1
STY4528 family pathogenicity island replication protein
COORDINATES: similar to AA sequence:RefSeq:WP_013199791.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199792.1
COORDINATES: similar to AA sequence:RefSeq:WP_007885452.1
SPI-7-type island replicative DNA helicase
COORDINATES: similar to AA sequence:RefSeq:WP_007885455.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015056497.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199796.1
COORDINATES: protein motif:HMM:TIGR03760.1
COORDINATES: protein motif:HMM:NF024685.2
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF019997.2
COORDINATES: similar to AA sequence:RefSeq:WP_013199804.1
COORDINATES: similar to AA sequence:RefSeq:WP_007885472.1
COORDINATES: similar to AA sequence:RefSeq:WP_000361425.1
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_000051067.1
COORDINATES: similar to AA sequence:RefSeq:WP_000864791.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612015.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_000168322.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF018044.2
conjugation system SOS inhibitor PsiB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003851710.1
anti-phage defense-associated sirtuin Dsr1
COORDINATES: protein motif:HMM:NF016370.2
COORDINATES: similar to AA sequence:RefSeq:WP_000611691.1
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_001562885.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611553.1
GO:0015074 - DNA integration [Evidence IEA]
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.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_008806992.1
COORDINATES: similar to AA sequence:RefSeq:WP_013196199.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010670287.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
GO:0004803 - transposase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012540156.1
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.