Kosakonia pseudosacchari strain BDA62-3 plasmid pBDA62-3, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Kosakonia.
Genome sequencings of bacterial endophytes
Submitted (20-OCT-2020) Department of Biology, University of Florence, via Madonna del Piano 6, Sesto Fiorentino 50019, Italy
REFSEQ INFORMATION: The reference sequence is identical to\nCP063426.1.\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 :: 14-OCT-2020\nAssembly Method :: HGAP v. Microbial Assembly 8.0.0.80529\nAssembly Name :: full assembly\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 141x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/16/2022 03:26:50\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) :: 4,784\nCDSs (total) :: 4,669\nGenes (coding) :: 4,626\nCDSs (with protein) :: 4,626\nGenes (RNA) :: 115\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 82\nncRNAs :: 11\nPseudo Genes (total) :: 43\nCDSs (without protein) :: 43\nPseudo Genes (ambiguous residues) :: 0 of 43\nPseudo Genes (frameshifted) :: 17 of 43\nPseudo Genes (incomplete) :: 29 of 43\nPseudo Genes (internal stop) :: 12 of 43\nPseudo Genes (multiple problems) :: 14 of 43\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_016495596.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016495597.1
COORDINATES: similar to AA sequence:RefSeq:WP_008325086.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_016495602.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_015572089.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_016495604.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_008324958.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_016495606.1
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_016495607.1
COORDINATES: similar to AA sequence:RefSeq:WP_008324961.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495609.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013087187.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014063862.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495620.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495621.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495623.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495624.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495625.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495627.1
COORDINATES: similar to AA sequence:RefSeq:WP_001569883.1
COORDINATES: similar to AA sequence:RefSeq:WP_007853275.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495506.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495507.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017891108.1
COORDINATES: similar to AA sequence:RefSeq:WP_017802585.1
COORDINATES: similar to AA sequence:RefSeq:WP_000776034.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008502211.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_000807689.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495515.1
COORDINATES: similar to AA sequence:RefSeq:WP_000241708.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495517.1
COORDINATES: similar to AA sequence:RefSeq:WP_004150768.1
COORDINATES: similar to AA sequence:RefSeq:WP_009654831.1
COORDINATES: protein motif:HMM:NF014244.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
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_001292425.1
COORDINATES: similar to AA sequence:RefSeq:WP_001568023.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229664.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016495570.1
COORDINATES: similar to AA sequence:RefSeq:WP_020322880.1
COORDINATES: similar to AA sequence:RefSeq:WP_011846847.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008502231.1
COORDINATES: similar to AA sequence:RefSeq:WP_000108588.1
COORDINATES: similar to AA sequence:RefSeq:WP_008502230.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016246488.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002431133.1
COORDINATES: similar to AA sequence:RefSeq:WP_000039982.1
COORDINATES: similar to AA sequence:RefSeq:WP_001194072.1
COORDINATES: similar to AA sequence:RefSeq:WP_016240531.1
COORDINATES: similar to AA sequence:RefSeq:WP_000872613.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_000090196.1
COORDINATES: similar to AA sequence:RefSeq:WP_000734115.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_006786768.1
COORDINATES: similar to AA sequence:RefSeq:WP_012113317.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006786772.1
COORDINATES: similar to AA sequence:RefSeq:WP_015839743.1
COORDINATES: similar to AA sequence:RefSeq:WP_012968890.1
COORDINATES: similar to AA sequence:RefSeq:WP_008927065.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322799.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988499.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_006120918.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495575.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016495576.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_003018683.1
GO:0019867 - outer membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016495579.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_016495580.1
conjugal transfer pilus assembly protein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_013087221.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495582.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495583.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495584.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495585.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_016495586.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_016495587.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_000833231.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_016495589.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843229.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495591.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495592.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495593.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_008325088.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_008325087.1