Pandoraea faecigallinarum strain DSM 23572 plasmid pPF72-2, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Pandoraea.
Complete Genome Sequence of Pandoraea faecigallinarum DSM-23572
Submitted (02-JUN-2016) Institute of Biological Sciences, University of Malaya, Jalan Universiti, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia
Submitted (11-JUN-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\nCP011809.2.\n\nOn Jun 12, 2016 this sequence version replaced NZ_CP011809.1.\nSource DNA and bacteria are available in Microbiome 3, High Impact\nResearch Building, University of Malaya, 50603 Kuala Lumpur (Chan\nKok Gan, kokgan@um.edu.my).\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. 35\nGenome Coverage :: 80.6X\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 02:34:08\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) :: 5,128\nCDSs (total) :: 5,046\nGenes (coding) :: 4,843\nCDSs (with protein) :: 4,843\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) :: 203\nCDSs (without protein) :: 203\nPseudo Genes (ambiguous residues) :: 0 of 203\nPseudo Genes (frameshifted) :: 60 of 203\nPseudo Genes (incomplete) :: 165 of 203\nPseudo Genes (internal stop) :: 22 of 203\nPseudo Genes (multiple problems) :: 42 of 203\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Pandoraea faecigallinarum
COORDINATES: similar to AA sequence:RefSeq:WP_003490888.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011345603.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_005931779.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
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_019303580.1
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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013688836.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012634672.1
COORDINATES: similar to AA sequence:RefSeq:WP_017172642.1
COORDINATES: similar to AA sequence:RefSeq:WP_017154897.1
COORDINATES: similar to AA sequence:RefSeq:WP_007735675.1
COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1
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_009916533.1
COORDINATES: protein motif:HMM:NF022104.2
COORDINATES: protein motif:HMM:NF013315.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_086557936.1
programmed frameshift; 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_007737248.1
COORDINATES: similar to AA sequence:RefSeq:WP_017424341.1
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: similar to AA sequence:RefSeq:WP_012837654.1
COORDINATES: protein motif:HMM:NF013676.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007182928.1
COORDINATES: similar to AA sequence:RefSeq:WP_019642187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011342942.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_007180432.1
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: protein motif:HMM:NF033546.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330561.1
COORDINATES: similar to AA sequence:RefSeq:WP_047389784.1
COORDINATES: similar to AA sequence:RefSeq:WP_006405231.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611899.1
COORDINATES: similar to AA sequence:RefSeq:WP_011515356.1
COORDINATES: similar to AA sequence:RefSeq:WP_011546517.1
COORDINATES: similar to AA sequence:RefSeq:WP_012222646.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017335482.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611267.1
COORDINATES: similar to AA sequence:RefSeq:WP_011154327.1
COORDINATES: similar to AA sequence:RefSeq:WP_013436660.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875954.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731385.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124610.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006713120.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009489204.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367242.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611673.1
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_012212959.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006762839.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012606398.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_076611183.1
COORDINATES: similar to AA sequence:RefSeq:WP_003151133.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310970.1
COORDINATES: similar to AA sequence:RefSeq:WP_011000219.1
COORDINATES: similar to AA sequence:RefSeq:WP_011882724.1
COORDINATES: similar to AA sequence:RefSeq:WP_011579009.1
COORDINATES: similar to AA sequence:RefSeq:WP_009238080.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182923.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_004526067.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007182944.1
COORDINATES: similar to AA sequence:RefSeq:WP_010206255.1
COORDINATES: similar to AA sequence:RefSeq:WP_005166025.1
type II toxin-antitoxin system MqsR family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010452730.1
type II toxin-antitoxin system MqsA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011548120.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011548121.1
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_018004499.1
COORDINATES: protein motif:HMM:NF017528.2
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: similar to AA sequence:RefSeq:WP_013700155.1
COORDINATES: similar to AA sequence:RefSeq:WP_017162391.1
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: similar to AA sequence:RefSeq:WP_013210022.1
COORDINATES: similar to AA sequence:RefSeq:WP_011004276.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495419.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014194526.1
COORDINATES: similar to AA sequence:RefSeq:WP_008345293.1
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_019303572.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194531.1
COORDINATES: similar to AA sequence:RefSeq:WP_017171755.1
COORDINATES: similar to AA sequence:RefSeq:WP_017160491.1