Caballeronia grimmiae strain Lep1A1 plasmid p4, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Caballeronia.
Prevalence and functional effects of a genomic island for insect symbiosis within Burkholderiaceae
Submitted (22-SEP-2021) Biology Department, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP084277.1.\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 Date :: 2020\nAssembly Method :: SPAdes v. 3.13.0; Unicycler v. 2.4.8-beta\nAssembly Name :: Lep1A1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 60x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 07:33:05\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 6,237\nCDSs (total) :: 6,157\nGenes (coding) :: 5,985\nCDSs (with protein) :: 5,985\nGenes (RNA) :: 80\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 4\nPseudo Genes (total) :: 172\nCDSs (without protein) :: 172\nPseudo Genes (ambiguous residues) :: 0 of 172\nPseudo Genes (frameshifted) :: 85 of 172\nPseudo Genes (incomplete) :: 110 of 172\nPseudo Genes (internal stop) :: 35 of 172\nPseudo Genes (multiple problems) :: 47 of 172\nCRISPR Arrays :: 2\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: protein motif:HMM:NF023898.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008343731.1
COORDINATES: protein motif:HMM:NF021982.2
GO:0005576 - extracellular region [Evidence IEA]
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016348557.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611570.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_018421064.1
COORDINATES: similar to AA sequence:RefSeq:WP_013435972.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014253109.1
COORDINATES: protein motif:HMM:NF028518.2
COORDINATES: similar to AA sequence:RefSeq:WP_007182868.1
COORDINATES: similar to AA sequence:RefSeq:WP_019143304.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344738.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194550.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014194549.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_014194548.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194547.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611495.1
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_076611305.1
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_010940725.1
COORDINATES: similar to AA sequence:RefSeq:WP_006482449.1
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:WP_076611734.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: protein motif:HMM:NF013014.2
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_011493645.1
COORDINATES: protein motif:HMM:NF013502.2
COORDINATES: similar to AA sequence:RefSeq:WP_017518763.1
COORDINATES: similar to AA sequence:RefSeq:WP_016346944.1
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612300.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551146.1
COORDINATES: protein motif:HMM:NF024244.2
COORDINATES: similar to AA sequence:RefSeq:WP_008961661.1
COORDINATES: similar to AA sequence:RefSeq:WP_017330817.1
COORDINATES: similar to AA sequence:RefSeq:WP_011490588.1
COORDINATES: similar to AA sequence:RefSeq:WP_020652927.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612098.1
programmed frameshift; 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_076611267.1
COORDINATES: similar to AA sequence:RefSeq:WP_011488770.1
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: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006482547.1
COORDINATES: similar to AA sequence:RefSeq:WP_018003639.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008350405.1
COORDINATES: similar to AA sequence:RefSeq:WP_009489732.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611601.1
COORDINATES: similar to AA sequence:RefSeq:WP_006757738.1
COORDINATES: similar to AA sequence:RefSeq:WP_012433247.1
COORDINATES: similar to AA sequence:RefSeq:WP_014253392.1
COORDINATES: similar to AA sequence:RefSeq:WP_007584088.1
COORDINATES: similar to AA sequence:RefSeq:WP_009770972.1
transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013334485.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013983520.1
COORDINATES: similar to AA sequence:RefSeq:WP_014597314.1
GO:0008767 - UDP-galactopyranose mutase activity [Evidence IEA]
GO:0009273 - peptidoglycan-based cell wall biogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612315.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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.
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
transposase zinc-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014253137.1
COORDINATES: similar to AA sequence:RefSeq:WP_011516698.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000311 - plastid large ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016347406.1
COORDINATES: similar to AA sequence:RefSeq:WP_016347174.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006894239.1
COORDINATES: similar to AA sequence:RefSeq:WP_008346630.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012433212.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493138.1
COORDINATES: similar to AA sequence:RefSeq:WP_008345251.1
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009396742.1
COORDINATES: similar to AA sequence:RefSeq:WP_012402327.1
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014193240.1
COORDINATES: protein motif:HMM:NF005559.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_016453639.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016453640.1
ribulose-bisphosphate carboxylase large subunit family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016453641.1
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013542288.1
COORDINATES: similar to AA sequence:RefSeq:WP_015666979.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013169049.1
COORDINATES: similar to AA sequence:RefSeq:WP_008960869.1
COORDINATES: similar to AA sequence:RefSeq:WP_006026423.1
COORDINATES: similar to AA sequence:RefSeq:WP_007596687.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018453582.1
GO:0016829 - lyase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019750927.1
COORDINATES: protein motif:HMM:NF022188.2
COORDINATES: similar to AA sequence:RefSeq:WP_007735675.1
COORDINATES: similar to AA sequence:RefSeq:WP_013089215.1
COORDINATES: similar to AA sequence:RefSeq:WP_020704288.1
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006047862.1
COORDINATES: similar to AA sequence:RefSeq:WP_020308560.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009770831.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009770832.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin