Candidatus Fukatsuia symbiotica strain 5D plasmid p5D_Fsymbiotica-3, complete sequence.
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\nCP021662.1.\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##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_006704792.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF014417.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
transcription termination/antitermination NusG family protein
COORDINATES: protein motif:HMM:NF017333.2
COORDINATES: similar to AA sequence:RefSeq:WP_006705581.1
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_001687089.1
COORDINATES: protein motif:HMM:NF022241.2
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873526.1
molybdopterin-guanine dinucleotide biosynthesis protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_012738248.1
COORDINATES: similar to AA sequence:RefSeq:WP_012738249.1
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_011214128.1
COORDINATES: protein motif:HMM:NF021943.2
COORDINATES: similar to AA sequence:RefSeq:WP_001196199.1
COORDINATES: similar to AA sequence:RefSeq:WP_011144720.1
GO:0004803 - transposase activity [Evidence IEA]
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:NF033590.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705839.1
COORDINATES: similar to AA sequence:RefSeq:WP_014543172.1
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_006707088.1
COORDINATES: similar to AA sequence:RefSeq:WP_012439747.1
COORDINATES: similar to AA sequence:RefSeq:WP_011846847.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024321.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
TcdA/TcdB catalytic glycosyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006706098.1
COORDINATES: similar to AA sequence:RefSeq:NP_462554.1
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:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_006707191.1
COORDINATES: protein motif:HMM:NF014814.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: similar to AA sequence:RefSeq:WP_041621276.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF022835.2
COORDINATES: similar to AA sequence:RefSeq:WP_013033472.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004514724.1
COORDINATES: protein motif:HMM:NF023713.2
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873477.1
COORDINATES: protein motif:HMM:NF033885.1
COORDINATES: protein motif:HMM:NF033883.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873079.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873078.1
COORDINATES: similar to AA sequence:RefSeq:WP_009408500.1
GO:0004540 - ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020801512.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_004131804.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017891135.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873481.1
COORDINATES: similar to AA sequence:RefSeq:WP_009651640.1
COORDINATES: similar to AA sequence:RefSeq:WP_012738258.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707032.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_018990404.1
COORDINATES: similar to AA sequence:RefSeq:WP_013743557.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873487.1
thioredoxin fold domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012738252.1
F-type conjugative transfer protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_007183062.1
COORDINATES: similar to AA sequence:RefSeq:WP_012806090.1
COORDINATES: similar to AA sequence:RefSeq:WP_011583148.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141593.1
frameshifted; 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_041412878.1
COORDINATES: similar to AA sequence:RefSeq:WP_001677640.1
COORDINATES: similar to AA sequence:RefSeq:WP_004703986.1