Caballeronia grimmiae strain Lep1A1 plasmid p5, 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\nCP084278.1.\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: similar to AA sequence:RefSeq:WP_006122481.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011013264.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_010676131.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114046.1
COORDINATES: similar to AA sequence:RefSeq:WP_000132020.1
regulatory protein for mating pair formation
COORDINATES: similar to AA sequence:RefSeq:WP_000283041.1
COORDINATES: similar to AA sequence:RefSeq:WP_000019167.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114072.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229638.1
mercury resistance transcriptional regulator MerR
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:WP_013722692.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001277466.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003132004.1
COORDINATES: similar to AA sequence:RefSeq:WP_003132006.1
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_086558120.1
GO:0004803 - transposase activity [Evidence IEA]
Tn3-like element IS1071 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011805354.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
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_008328818.1
IS91-like element ISPps1 family transposase
COORDINATES: protein motif:HMM:NF013465.2
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008477529.1
GO:0003866 - 3-phosphoshikimate 1-carboxyvinyltransferase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
3-phosphoshikimate 1-carboxyvinyltransferase
COORDINATES: nucleotide motif:Rfam:14.4:RF00162
SAM riboswitch class I; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012706.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011841290.1
COORDINATES: similar to AA sequence:RefSeq:WP_003067307.1
GO:0008776 - acetate kinase activity [Evidence IEA]
GO:0006083 - acetate metabolic process [Evidence IEA]; GO:0006113 - fermentation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024491.2
COORDINATES: similar to AA sequence:RefSeq:WP_013801159.1
COORDINATES: similar to AA sequence:RefSeq:WP_005796390.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011114071.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015913623.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011137973.1
COORDINATES: similar to AA sequence:RefSeq:WP_015913624.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114068.1
DNA binding protein involved in transcriptional regulation
COORDINATES: similar to AA sequence:RefSeq:WP_012478185.1
COORDINATES: similar to AA sequence:RefSeq:WP_015913627.1
COORDINATES: similar to AA sequence:RefSeq:WP_012478184.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798723.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890110.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114061.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890108.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011342948.1
COORDINATES: similar to AA sequence:RefSeq:WP_000664557.1
COORDINATES: similar to AA sequence:RefSeq:WP_000826922.1
COORDINATES: similar to AA sequence:RefSeq:WP_000718516.1
COORDINATES: similar to AA sequence:RefSeq:WP_011304098.1
COORDINATES: similar to AA sequence:RefSeq:WP_001127128.1
COORDINATES: similar to AA sequence:RefSeq:WP_000426567.1
conjugal transfer transcriptional regulator TraJ
COORDINATES: similar to AA sequence:RefSeq:WP_011137971.1
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_011655356.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000086826.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_011114056.1
GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]; GO:0098847 - sequence-specific single stranded DNA binding [Evidence IEA]
GO:0051304 - chromosome separation [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]; GO:0006261 - DNA-templated DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006122510.1
COORDINATES: similar to AA sequence:RefSeq:WP_006122509.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011178411.1
COORDINATES: similar to AA sequence:RefSeq:WP_001665065.1
GO:0042834 - peptidoglycan binding [Evidence IEA]; GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011798696.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798697.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798698.1
transglycosylase SLT domain-containing protein
probable role in the formation of the mating lock (cell-cell contact between donor and recipient) during conjugation on the basis that TrbM shows homology to Haemophilus influenzae adhesin and has an export signal sequence
COORDINATES: similar to AA sequence:RefSeq:WP_010890138.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_011114051.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_000644148.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009292 - horizontal gene transfer [Evidence IEA]
mating pair formation and entry exclusion
COORDINATES: similar to AA sequence:RefSeq:WP_000802794.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_011114050.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798704.1
COORDINATES: similar to AA sequence:RefSeq:WP_000753228.1
P-type conjugative transfer protein TrbG