Pandoraea vervacti strain NS15 plasmid pPV15, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Pandoraea.
Complete Genome Sequencing of Pandoraea vervacti NS15 sp. nov.
Submitted (17-NOV-2016) Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Kuala Lumpur 50603, Malaysia
Submitted (17-FEB-2015) Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Kuala Lumpur 50603, Malaysia
REFSEQ INFORMATION: The reference sequence is identical to\nCP010898.2.\n\nOn Dec 18, 2016 this sequence version replaced NZ_CP010898.1.\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 :: HGAP v. 2\nGenome Coverage :: 185x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 02:48:57\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) :: 4,985\nCDSs (total) :: 4,903\nGenes (coding) :: 4,825\nCDSs (with protein) :: 4,825\nGenes (RNA) :: 82\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 4\nPseudo Genes (total) :: 78\nCDSs (without protein) :: 78\nPseudo Genes (ambiguous residues) :: 0 of 78\nPseudo Genes (frameshifted) :: 19 of 78\nPseudo Genes (incomplete) :: 55 of 78\nPseudo Genes (internal stop) :: 8 of 78\nPseudo Genes (multiple problems) :: 4 of 78\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_007974938.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008343663.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005931796.1
COORDINATES: similar to AA sequence:RefSeq:WP_007968755.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017161284.1
COORDINATES: similar to AA sequence:RefSeq:WP_017160491.1
COORDINATES: similar to AA sequence:RefSeq:WP_003490888.1
COORDINATES: similar to AA sequence:RefSeq:WP_011052985.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_005931779.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343655.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014194537.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007966857.1
COORDINATES: similar to AA sequence:RefSeq:WP_017172140.1
COORDINATES: similar to AA sequence:RefSeq:WP_017164708.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004542720.1
COORDINATES: similar to AA sequence:RefSeq:WP_013688836.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012339753.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017172642.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017154897.1
COORDINATES: protein motif:HMM:NF023208.2
COORDINATES: similar to AA sequence:RefSeq:WP_018419515.1
COORDINATES: similar to AA sequence:RefSeq:WP_011883416.1
COORDINATES: similar to AA sequence:RefSeq:WP_017235271.1
COORDINATES: similar to AA sequence:RefSeq:WP_008164395.1
COORDINATES: similar to AA sequence:RefSeq:WP_006224317.1
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: similar to AA sequence:RefSeq:WP_008351964.1
COORDINATES: similar to AA sequence:RefSeq:WP_006219523.1
COORDINATES: similar to AA sequence:RefSeq:WP_000994919.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ParB/Srx family N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011544710.1
COORDINATES: similar to AA sequence:RefSeq:WP_013588587.1
COORDINATES: similar to AA sequence:RefSeq:WP_012493229.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_020309499.1
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_004553608.1
COORDINATES: similar to AA sequence:RefSeq:WP_013394638.1
COORDINATES: similar to AA sequence:RefSeq:WP_016715835.1
COORDINATES: similar to AA sequence:RefSeq:WP_009523744.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558222.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018442479.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: protein motif:HMM:TIGR00229.1
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_011563055.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: protein motif:HMM:NF012257.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017234432.1
COORDINATES: similar to AA sequence:RefSeq:WP_014724924.1
COORDINATES: similar to AA sequence:RefSeq:WP_006484966.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611305.1
COORDINATES: similar to AA sequence:RefSeq:WP_012430381.1
COORDINATES: similar to AA sequence:RefSeq:WP_013698113.1
COORDINATES: protein motif:HMM:NF016836.2
COORDINATES: similar to AA sequence:RefSeq:WP_017234467.1
COORDINATES: similar to AA sequence:RefSeq:WP_012377295.1
hydrogenase expression/formation protein HypE
COORDINATES: similar to AA sequence:RefSeq:WP_014068053.1
GO:0016530 - metallochaperone activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018175937.1
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_012845076.1
GO:0003998 - acylphosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017774735.1
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_017774734.1
COORDINATES: similar to AA sequence:RefSeq:WP_014433201.1
GO:0016151 - nickel cation binding [Evidence IEA]
nickel-dependent hydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012699123.1
COORDINATES: similar to AA sequence:RefSeq:WP_014068047.1
COORDINATES: similar to AA sequence:RefSeq:WP_017774730.1
cyclic nucleotide-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016920199.1
4Fe-4S dicluster domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007735681.1
COORDINATES: protein motif:HMM:NF026288.2
COORDINATES: similar to AA sequence:RefSeq:WP_001686642.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003490780.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
BsuBI/PstI family type II restriction endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_014252906.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182875.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013691838.1
COORDINATES: similar to AA sequence:RefSeq:WP_010316356.1
COORDINATES: similar to AA sequence:RefSeq:WP_018990404.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019564015.1
COORDINATES: similar to AA sequence:RefSeq:WP_017160511.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF009888.0
COORDINATES: similar to AA sequence:RefSeq:WP_012354406.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612300.1
COORDINATES: protein motif:HMM:NF012699.2
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF021514.2
COORDINATES: similar to AA sequence:RefSeq:WP_011003443.1
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: similar to AA sequence:RefSeq:WP_012405348.1
COORDINATES: protein motif:HMM:NF019846.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014795.2
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]