Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum) plasmid pHD5AT, complete sequence.
Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; aphid secondary symbionts; Candidatus Hamiltonella.
Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors
Submitted (05-DEC-2008) Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St, Tucson, AZ 85721-0088, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001278.1.\nDNA Source: Nancy Moran, University of Arizona.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 13:47:51\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) :: 2,212\nCDSs (total) :: 2,158\nGenes (coding) :: 2,001\nCDSs (with protein) :: 2,001\nGenes (RNA) :: 54\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 41\nncRNAs :: 4\nPseudo Genes (total) :: 157\nCDSs (without protein) :: 157\nPseudo Genes (ambiguous residues) :: 1 of 157\nPseudo Genes (frameshifted) :: 64 of 157\nPseudo Genes (incomplete) :: 107 of 157\nPseudo Genes (internal stop) :: 32 of 157\nPseudo Genes (multiple problems) :: 39 of 157\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012738240.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_015873553.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006703981.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873804.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0006298 - mismatch repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015873589.1
COORDINATES: similar to AA sequence:RefSeq:WP_000147566.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704027.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704028.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_000470624.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002209739.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_005918230.1
COORDINATES: similar to AA sequence:RefSeq:WP_015874472.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857841.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873284.1
COORDINATES: similar to AA sequence:RefSeq:WP_012738249.1
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_012737993.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857839.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015873280.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873279.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873487.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857858.1
COORDINATES: similar to AA sequence:RefSeq:WP_019080654.1
COORDINATES: protein motif:HMM:NF016876.2
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016857860.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_016857861.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873481.1
COORDINATES: similar to AA sequence:RefSeq:WP_002556016.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873479.1
COORDINATES: similar to AA sequence:RefSeq:WP_012755126.1
COORDINATES: similar to AA sequence:RefSeq:WP_009622956.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873078.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873079.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873080.1
COORDINATES: protein motif:HMM:NF033885.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873477.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873476.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873475.1
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_016857590.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873827.1
type IV secretion system DotC family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873828.1
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_015873829.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873830.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873831.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873832.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_015873833.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873462.1
too many ambiguous residues; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873097.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873098.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015873836.1
COORDINATES: similar to AA sequence:RefSeq:WP_020483566.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873458.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988414.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_016858107.1
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: protein motif:HMM:NF014417.2
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873761.1
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873106.1