Serratia symbiotica strain 24.1 plasmid pSsAf24.1-1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Serratia.
At the gate of mutualism: identification of genomic traits predisposing to insect-bacterial symbiosis in pathogenic strains of the aphid symbiont Serratia symbiotica
Submitted (31-MAR-2021) Earth and Life Institute, Universite catholique de Louvain, Carnoy Croix du sud 4-5/L7.07.04, Louvain-la-Neuve 1348, Belgium
Submitted (01-APR-2020) Earth and Life Institute, Universite Catholique de Louvain, Carnoy Croix du Sud 4-5/L7.07.04, Louvain-la-Neuve 1348, Belgium
REFSEQ INFORMATION: The reference sequence is identical to\nCP072650.1.\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 Method :: Unicycler v. v0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 116.0x\nSequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/10/2023 23:36:40\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) :: 3,106\nCDSs (total) :: 3,011\nGenes (coding) :: 2,672\nCDSs (with protein) :: 2,672\nGenes (RNA) :: 95\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 69\nncRNAs :: 4\nPseudo Genes (total) :: 339\nCDSs (without protein) :: 339\nPseudo Genes (ambiguous residues) :: 0 of 339\nPseudo Genes (frameshifted) :: 199 of 339\nPseudo Genes (incomplete) :: 225 of 339\nPseudo Genes (internal stop) :: 132 of 339\nPseudo Genes (multiple problems) :: 176 of 339\nCRISPR Arrays :: 1\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+.
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF020384.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF016785.2
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_017119528.1
COORDINATES: protein motif:HMM:NF013878.2
COORDINATES: similar to AA sequence:RefSeq:WP_011988545.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF019997.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014168902.1
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_004245074.1
COORDINATES: similar to AA sequence:RefSeq:WP_012311706.1
COORDINATES: similar to AA sequence:RefSeq:WP_016528790.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014043.2
COORDINATES: similar to AA sequence:RefSeq:WP_017844503.1
COORDINATES: similar to AA sequence:RefSeq:WP_019486767.1
COORDINATES: similar to AA sequence:RefSeq:WP_012769229.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF017103.2
COORDINATES: similar to AA sequence:RefSeq:WP_004876397.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000517490.1
COORDINATES: protein motif:HMM:NF040300.1
COORDINATES: similar to AA sequence:RefSeq:WP_001125903.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR04346.1
type IV secretion system protein IcmP/DotM
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: similar to AA sequence:RefSeq:WP_006663557.1
COORDINATES: protein motif:HMM:NF020355.2
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011988519.1
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: protein motif:HMM:NF022835.2
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_011988506.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_011988555.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988595.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988571.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988611.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013014.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_019438929.1
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011988520.1
COORDINATES: protein motif:HMM:NF025241.2
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011988525.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988594.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988605.1
COORDINATES: similar to AA sequence:RefSeq:WP_004356320.1
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011988569.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF019064.2
COORDINATES: protein motif:HMM:NF022136.2
COORDINATES: similar to AA sequence:RefSeq:WP_011988515.1
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: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:TIGR03021.1
GO:0009297 - pilus assembly [Evidence IEA]