Candidatus Fukatsuia symbiotica strain 5D plasmid p5D_Fsymbiotica-1, 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\nCP021660.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011144720.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611597.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: similar to AA sequence:RefSeq:WP_017030086.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704154.1
COORDINATES: protein motif:HMM:NF017333.2
COORDINATES: protein motif:HMM:NF026057.2
transposase DNA-binding-containing protein
COORDINATES: protein motif:HMM:NF033590.1
COORDINATES: similar to AA sequence:RefSeq:WP_002813607.1
COORDINATES: protein motif:HMM:NF013842.2
COORDINATES: protein motif:HMM:NF025079.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015873826.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704235.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873484.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006707031.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015873482.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: similar to AA sequence:RefSeq:WP_009651640.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873481.1
COORDINATES: similar to AA sequence:RefSeq:WP_017891135.1
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_010100359.1
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015873587.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015873078.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873079.1
COORDINATES: protein motif:HMM:NF033883.1
COORDINATES: protein motif:HMM:NF033885.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873477.1
COORDINATES: similar to AA sequence:RefSeq:WP_000751782.1
DotH/IcmK family type IV secretion protein
COORDINATES: protein motif:HMM:NF022835.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873474.1
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873087.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857588.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010105669.1
COORDINATES: similar to AA sequence:RefSeq:WP_012368699.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017891019.1
type IV secretion system DotC family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004720812.1
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000165970.1
Rop family plasmid primer RNA-binding protein
COORDINATES: protein motif:HMM:NF016785.2
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014606847.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001585135.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705281.1
COORDINATES: protein motif:HMM:NF012257.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: protein motif:HMM:NF003417.0
COORDINATES: similar to AA sequence:RefSeq:WP_015080894.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_003484733.1
COORDINATES: similar to AA sequence:RefSeq:WP_014631174.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:1904680 - peptide transmembrane transporter activity [Evidence IEA]
GO:0015833 - peptide transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01733.1
amino acid adenylation domain-containing protein
COORDINATES: protein motif:HMM:NF016377.2
COORDINATES: protein motif:HMM:TIGR01426.1
GO:0016758 - hexosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013166.2
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010110933.1
aspartyl/asparaginyl beta-hydroxylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020568317.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014725941.1
COORDINATES: protein motif:HMM:NF014349.2
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611885.1
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_014611598.1
COORDINATES: similar to AA sequence:RefSeq:WP_006118548.1
COORDINATES: similar to AA sequence:RefSeq:WP_000389249.1
COORDINATES: protein motif:HMM:NF013760.2
MotA/TolQ/ExbB proton channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016857221.1
COORDINATES: similar to AA sequence:RefSeq:WP_001080577.1
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:NP_463127.1
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.
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013124600.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_003155746.1
COORDINATES: similar to AA sequence:RefSeq:WP_011517528.1
COORDINATES: similar to AA sequence:RefSeq:WP_017412822.1
COORDINATES: similar to AA sequence:RefSeq:WP_010304095.1
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:NF024907.2
COORDINATES: similar to AA sequence:RefSeq:WP_006704290.1
COORDINATES: similar to AA sequence:RefSeq:WP_012767883.1
COORDINATES: similar to AA sequence:RefSeq:WP_005968053.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_019486655.1
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012776405.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705581.1
COORDINATES: similar to AA sequence:RefSeq:WP_010378701.1
COORDINATES: similar to AA sequence:RefSeq:WP_041621276.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_001603134.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011146873.1
COORDINATES: similar to AA sequence:RefSeq:WP_012790668.1
COORDINATES: similar to AA sequence:RefSeq:WP_011846847.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012439747.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707088.1
COORDINATES: protein motif:HMM:NF023077.2
membrane-targeted effector domain-containing toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017173693.1
COORDINATES: similar to AA sequence:RefSeq:WP_014003879.1
COORDINATES: similar to AA sequence:RefSeq:WP_017465947.1
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_004948414.1
COORDINATES: similar to AA sequence:RefSeq:NP_463182.1
COORDINATES: similar to AA sequence:RefSeq:WP_014030534.1
COORDINATES: similar to AA sequence:RefSeq:WP_006707570.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705642.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006705643.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: protein motif:HMM:NF024935.2
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_014333818.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333819.1