Pandoraea apista strain DSM 16535 plasmid pPA35, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Pandoraea.
Complete genome sequence of Pandoraea apista DSM 16535
Submitted (05-DEC-2016) Institute of Biological Sciences, University of Malaya, Jalan Universiti, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia
Submitted (07-DEC-2015) Institute of Biological Sciences, University of Malaya, Jalan Universiti, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia
REFSEQ INFORMATION: The reference sequence is identical to\nCP013482.1.\n\nSource bacteria is available from Microbiome 3, High Impact\nResearch Building, University of Malaya, 50603 Kuala Lumpur.\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 :: HGAP v. 3\nGenome Coverage :: 237.83x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 03:00:58\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) :: 5,058\nCDSs (total) :: 4,977\nGenes (coding) :: 4,897\nCDSs (with protein) :: 4,897\nGenes (RNA) :: 81\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 65\nncRNAs :: 4\nPseudo Genes (total) :: 80\nCDSs (without protein) :: 80\nPseudo Genes (ambiguous residues) :: 0 of 80\nPseudo Genes (frameshifted) :: 13 of 80\nPseudo Genes (incomplete) :: 72 of 80\nPseudo Genes (internal stop) :: 9 of 80\nPseudo Genes (multiple problems) :: 11 of 80\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011851228.1
frameshifted; 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.
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]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006401402.1
COORDINATES: similar to AA sequence:RefSeq:WP_006762649.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013958804.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system VapC family toxin
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011875925.1
COORDINATES: similar to AA sequence:RefSeq:WP_012824448.1
COORDINATES: similar to AA sequence:RefSeq:WP_004636893.1
COORDINATES: similar to AA sequence:RefSeq:WP_012430942.1
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: similar to AA sequence:RefSeq:WP_014194221.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875985.1
COORDINATES: similar to AA sequence:RefSeq:WP_003265798.1
COORDINATES: similar to AA sequence:RefSeq:WP_014579490.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017161201.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019842063.1
COORDINATES: similar to AA sequence:RefSeq:WP_004196194.1
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_011205817.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017173892.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014708279.1
conjugal transfer transcriptional regulator TraJ
COORDINATES: similar to AA sequence:RefSeq:WP_017161206.1
COORDINATES: similar to AA sequence:RefSeq:WP_010676180.1
COORDINATES: protein motif:HMM:NF010470.0
COORDINATES: similar to AA sequence:RefSeq:WP_011342948.1
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_017160971.1
COORDINATES: protein motif:HMM:NF014691.2
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_003019726.1
COORDINATES: similar to AA sequence:RefSeq:WP_017166876.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010676187.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890110.1
COORDINATES: protein motif:HMM:NF036636.2
COORDINATES: similar to AA sequence:RefSeq:WP_006999574.1
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_017161448.1
COORDINATES: similar to AA sequence:RefSeq:WP_011255084.1
COORDINATES: similar to AA sequence:RefSeq:WP_001665082.1
COORDINATES: similar to AA sequence:RefSeq:WP_017168819.1
COORDINATES: similar to AA sequence:RefSeq:WP_010676131.1
COORDINATES: similar to AA sequence:RefSeq:WP_017166904.1
type IV secretion system ATPase VirB4 family; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: similar to AA sequence:RefSeq:WP_011255078.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_017161251.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114050.1
COORDINATES: similar to AA sequence:RefSeq:WP_003019633.1
P-type conjugative transfer protein TrbJ
COORDINATES: protein motif:HMM:TIGR02783.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_005027717.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_010894501.1
COORDINATES: similar to AA sequence:RefSeq:WP_020308563.1
COORDINATES: protein motif:HMM:NF023351.2
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_011487248.1