Serratia symbiotica strain 24.1 plasmid pSsAf24.1-2, 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\nCP072651.1.\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: similar to AA sequence:RefSeq:WP_019079014.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004363 - glutathione synthase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0006750 - glutathione biosynthetic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:NP_311849.2
GO:0008168 - methyltransferase activity [Evidence IEA]
GO:0006364 - rRNA processing [Evidence IEA]
16S rRNA (uracil(1498)-N(3))-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_020884599.1
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:YP_005226772.1
GO:0016740 - transferase activity [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.
COORDINATES: similar to AA sequence:RefSeq:WP_004711175.1
GO:0008951 - palmitoleoyl [acyl-carrier-protein]-dependent acyltransferase activity [Evidence IEA]
GO:0036104 - Kdo2-lipid A biosynthetic process [Evidence IEA]; GO:0009409 - response to cold [Evidence IEA]
kdo(2)-lipid IV(A) palmitoleoyltransferase
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017412.2
COORDINATES: similar to AA sequence:RefSeq:WP_002214647.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
zinc uptake transcriptional repressor Zur
COORDINATES: similar to AA sequence:RefSeq:WP_015379224.1
GO:0015297 - antiporter activity [Evidence IEA]; GO:0042910 - xenobiotic transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015869689.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006282 - regulation of DNA repair [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013814749.1
COORDINATES: similar to AA sequence:RefSeq:WP_015379226.1
GO:0004366 - glycerol-3-phosphate O-acyltransferase activity [Evidence IEA]
GO:0008654 - phospholipid biosynthetic process [Evidence IEA]
glycerol-3-phosphate 1-O-acyltransferase PlsB
COORDINATES: similar to AA sequence:RefSeq:WP_006708061.1
GO:0008412 - 4-hydroxybenzoate octaprenyltransferase activity [Evidence IEA]
GO:0006744 - ubiquinone biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006708060.1
GO:0008813 - chorismate lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004705333.1
GO:0004347 - glucose-6-phosphate isomerase activity [Evidence IEA]
GO:0006094 - gluconeogenesis [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00168
Lysine riboswitch is most abundant in Firmicutes and Gammaproteobacteria where they are found upstream of a number of genes involved in lysine biosynthesis, transport and catabolism; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_015962105.1
GO:0004072 - aspartate kinase activity [Evidence IEA]
GO:0009089 - lysine biosynthetic process via diaminopimelate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013200333.1
COORDINATES: similar to AA sequence:RefSeq:WP_015841906.1
GO:0008899 - homoserine O-succinyltransferase activity [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00001
Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: nucleotide motif:Rfam:14.4:RF02541
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: nucleotide motif:Rfam:14.4:RF00177
COORDINATES: similar to AA sequence:RefSeq:WP_006709205.1
menaquinone-dependent protoporphyrinogen IX dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:NP_312804.1
COORDINATES: similar to AA sequence:RefSeq:WP_002211547.1
COORDINATES: similar to AA sequence:RefSeq:WP_004167939.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016929443.1
GO:0016831 - carboxy-lyase activity [Evidence IEA]
4-hydroxy-3-polyprenylbenzoate decarboxylase
COORDINATES: similar to AA sequence:RefSeq:WP_012477181.1
COORDINATES: similar to AA sequence:RefSeq:WP_015344010.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611197.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; 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_006322873.1
COORDINATES: similar to AA sequence:RefSeq:WP_016929586.1
COORDINATES: similar to AA sequence:RefSeq:WP_006321735.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012004539.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322895.1
COORDINATES: similar to AA sequence:RefSeq:WP_013204507.1
GO:0009345 - glycine-tRNA ligase complex [Evidence IEA]
GO:0004820 - glycine-tRNA ligase activity [Evidence IEA]
GO:0006426 - glycyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_462555.1
COORDINATES: similar to AA sequence:RefSeq:WP_009151157.1
internal stop; 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_019455519.1
COORDINATES: similar to AA sequence:RefSeq:WP_004950639.1
catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; subunit IIC forms the translocation channel and contains the specific substrate-binding site; subunit IIA is phosphorylated and transfers the phosphoryl group to the IIB subunit; subunit IIB transfers the phosphoryl group to the substrate; frameshifted; 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_013365374.1
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_076611102.1
COORDINATES: similar to AA sequence:RefSeq:WP_006708733.1
GO:0051989 - coproporphyrinogen dehydrogenase activity [Evidence IEA]
GO:0006779 - porphyrin-containing compound biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011095132.1
GO:0016462 - pyrophosphatase activity [Evidence IEA]
RdgB/HAM1 family non-canonical purine NTP pyrophosphatase
COORDINATES: similar to AA sequence:RefSeq:WP_006708735.1
COORDINATES: similar to AA sequence:RefSeq:WP_012413935.1
COORDINATES: similar to AA sequence:RefSeq:WP_004391012.1
GO:0004735 - pyrroline-5-carboxylate reductase activity [Evidence IEA]
GO:0006561 - proline biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004958752.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
YggS family pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_017803489.1
type IV pilus twitching motility protein PilT
COORDINATES: similar to AA sequence:RefSeq:WP_002209978.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012442535.1