Candidatus Fukatsuia symbiotica strain 5D plasmid p5D_Fsymbiotica-2.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Candidatus Fukatsuia.
Genome sequence of Candidatus Fukatsuia symbiotica and Candidatus Hamiltonella defensa from Acyrthosiphon pisum strain 5D
Submitted (30-MAY-2017) Department of Entomology, The University of Georgia, 120 Cedar St, Athens, GA 30602, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP021661.1.\nBacteria and source DNA available from Kerry M. Oliver, 120 Cedar\nStreet, 413 Biological Sciences Building, Athens, 30602,GA.\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 :: 15-MAY-2017\nAssembly Method :: HGAP.3 v. 3\nAssembly Name :: 5D_Xtype\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 290.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/18/2023 02:52:12\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) :: 3,119\nCDSs (total) :: 3,050\nGenes (coding) :: 2,663\nCDSs (with protein) :: 2,663\nGenes (RNA) :: 69\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 387\nCDSs (without protein) :: 387\nPseudo Genes (ambiguous residues) :: 0 of 387\nPseudo Genes (frameshifted) :: 241 of 387\nPseudo Genes (incomplete) :: 170 of 387\nPseudo Genes (internal stop) :: 43 of 387\nPseudo Genes (multiple problems) :: 57 of 387\n##Genome-Annotation-Data-END##
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF022183.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012738240.1
COORDINATES: similar to AA sequence:RefSeq:WP_013220547.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004091417.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873536.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707375.1
COORDINATES: similar to AA sequence:RefSeq:WP_001433474.1
COORDINATES: similar to AA sequence:RefSeq:WP_011144720.1
COORDINATES: similar to AA sequence:RefSeq:WP_005369975.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF036629.2
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_003142901.1
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_001773445.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_006707076.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707077.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857443.1
COORDINATES: similar to AA sequence:RefSeq:WP_001623617.1
COORDINATES: similar to AA sequence:RefSeq:WP_002667247.1
COORDINATES: similar to AA sequence:RefSeq:WP_011191426.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003151133.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018310970.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011988434.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873092.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873831.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988423.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_011988446.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873833.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873095.1
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011988476.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873098.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:NF015807.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873100.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873458.1
COORDINATES: similar to AA sequence:RefSeq:WP_004171982.1
COORDINATES: similar to AA sequence:RefSeq:WP_015446388.1
COORDINATES: similar to AA sequence:RefSeq:WP_004359135.1
COORDINATES: protein motif:HMM:NF012485.2
COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000754361.1
TrbM/KikA/MpfK family conjugal transfer protein
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_001773466.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017684943.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705279.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_006705278.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705276.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705835.1
COORDINATES: similar to AA sequence:RefSeq:WP_016858020.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006705833.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006705272.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006707616.1
COORDINATES: similar to AA sequence:RefSeq:WP_016233494.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016857450.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006705832.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705831.1
VirB4 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF016957.2
COORDINATES: similar to AA sequence:RefSeq:WP_006705829.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707622.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873841.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873760.1
COORDINATES: similar to AA sequence:RefSeq:WP_015874496.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015873106.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873107.1
plasmid replication initiator-like protein
COORDINATES: similar to AA sequence:RefSeq:WP_006705187.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704151.1
COORDINATES: protein motif:HMM:NF013752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: similar to AA sequence:RefSeq:WP_006707012.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707013.1
COORDINATES: similar to AA sequence:RefSeq:WP_011839971.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188411.1
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_007348006.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707138.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006705839.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141593.1
COORDINATES: similar to AA sequence:RefSeq:WP_015379150.1
COORDINATES: similar to AA sequence:RefSeq:WP_016930174.1
COORDINATES: similar to AA sequence:RefSeq:WP_008581469.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
COORDINATES: protein motif:HMM:NF023985.2
ribbon-helix-helix domain-containing protein
COORDINATES: protein motif:HMM:NF016876.2
COORDINATES: similar to AA sequence:RefSeq:WP_006704154.1
COORDINATES: similar to AA sequence:RefSeq:WP_006706936.1
COORDINATES: similar to AA sequence:RefSeq:WP_019428295.1
COORDINATES: similar to AA sequence:RefSeq:WP_019428294.1
frameshifted; incomplete; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.