Salmonella bongori N268-08 plasmid RM1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella.
Genome sequence of Salmonella bongori N268-08 - a rare clinical isolate
Submitted (03-JUL-2013) ETH zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich 8092, Switzerland
REFSEQ INFORMATION: The reference sequence is identical to\nCP006609.1.\nBacteria are available from the Swiss National Center for\nEnteropathogenic Bacteria and Listeria (NENT). DNA is available\nfrom the submitter's laboratory.\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 :: SMRTanalysis v. 2.01\nGenome Coverage :: 25x; 300x\nSequencing Technology :: PacBio; IonTorrent; Sanger\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 01:47:19\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) :: 4,618\nCDSs (total) :: 4,501\nGenes (coding) :: 4,336\nCDSs (with protein) :: 4,336\nGenes (RNA) :: 117\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 86\nncRNAs :: 9\nPseudo Genes (total) :: 165\nCDSs (without protein) :: 165\nPseudo Genes (ambiguous residues) :: 0 of 165\nPseudo Genes (frameshifted) :: 78 of 165\nPseudo Genes (incomplete) :: 110 of 165\nPseudo Genes (internal stop) :: 38 of 165\nPseudo Genes (multiple problems) :: 48 of 165\nPseudo Genes (short protein) :: 1 of 165\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012543393.1
GO:0015074 - DNA integration [Evidence IEA]
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.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:NP_490498.3
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.
COORDINATES: similar to AA sequence:RefSeq:NP_490495.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:NP_449411.1
COORDINATES: protein motif:HMM:NF017655.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
type-F conjugative transfer system pilin acetylase TraX
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
IncF plasmid conjugative transfer pilin acetylase TraX
COORDINATES: similar to AA sequence:RefSeq:WP_000766821.1
COORDINATES: similar to AA sequence:RefSeq:WP_000949137.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_001733785.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_001485398.1
conjugal transfer complement resistance protein TraT
COORDINATES: similar to AA sequence:RefSeq:WP_032490372.1
COORDINATES: similar to AA sequence:RefSeq:WP_000257544.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_001808382.1
conjugal transfer pilus assembly protein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_001525738.1
type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_001403279.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_000821868.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_000832511.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_001525842.1
COORDINATES: similar to AA sequence:RefSeq:WP_016529742.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_001525788.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_004558355.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_000714154.1
COORDINATES: similar to AA sequence:RefSeq:WP_000724456.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_008455349.1
COORDINATES: protein motif:HMM:NF018947.2
COORDINATES: similar to AA sequence:RefSeq:WP_001525693.1
ATP-dependent protease Clp ATPase subunit
COORDINATES: similar to AA sequence:RefSeq:WP_000786061.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000024510.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_008455355.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_001395451.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_032490353.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_008455360.1
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_008455362.1
COORDINATES: similar to AA sequence:RefSeq:WP_008455364.1
conjugal transfer relaxosome DNA-binding protein TraM
COORDINATES: similar to AA sequence:RefSeq:WP_008455366.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000556933.1
COORDINATES: similar to AA sequence:RefSeq:WP_000080850.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001403164.1
COORDINATES: similar to AA sequence:RefSeq:WP_008455374.1
COORDINATES: similar to AA sequence:RefSeq:WP_008455376.1
COORDINATES: similar to AA sequence:RefSeq:WP_000872088.1
COORDINATES: similar to AA sequence:RefSeq:WP_000611691.1
COORDINATES: similar to AA sequence:RefSeq:NP_490557.1
COORDINATES: similar to AA sequence:RefSeq:WP_002211744.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:NP_490555.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229748.1
COORDINATES: similar to AA sequence:RefSeq:WP_001310283.1
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_004118473.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229756.1
COORDINATES: similar to AA sequence:RefSeq:WP_001027499.1
COORDINATES: similar to AA sequence:RefSeq:WP_000108571.1
COORDINATES: similar to AA sequence:RefSeq:WP_001198918.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322848.1
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_008322847.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229762.1
COORDINATES: similar to AA sequence:RefSeq:NP_958723.1
COORDINATES: similar to AA sequence:RefSeq:NP_490548.1
COORDINATES: similar to AA sequence:RefSeq:WP_004194745.1
COORDINATES: similar to AA sequence:RefSeq:NP_490546.1
COORDINATES: similar to AA sequence:RefSeq:NP_490545.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:NP_490544.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:YP_005229774.1
COORDINATES: similar to AA sequence:RefSeq:NP_490542.1
COORDINATES: similar to AA sequence:RefSeq:NP_490541.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003119931.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF036772.2
COORDINATES: protein motif:HMM:NF014114.2
COORDINATES: similar to AA sequence:RefSeq:NP_490521.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_490520.1
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:NP_490518.1
type II toxin-antitoxin system toxin CcdB
COORDINATES: similar to AA sequence:RefSeq:NP_490517.1
type II toxin-antitoxin system antitoxin CcdA
COORDINATES: similar to AA sequence:RefSeq:YP_005229629.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_000815114.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF012698.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR01414.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015474 - autotransporter activity [Evidence IEA]
GO:0046819 - protein secretion by the type V secretion system [Evidence IEA]
autotransporter outer membrane beta-barrel domain-containing protein
Vi polysaccharide biosynthesis protein tviA
COORDINATES: similar to AA sequence:RefSeq:NP_415949.3
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; 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_076611553.1
COORDINATES: similar to AA sequence:RefSeq:WP_001539782.1
COORDINATES: similar to AA sequence:RefSeq:WP_000348879.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001585051.1
COORDINATES: similar to AA sequence:RefSeq:NP_490513.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:NP_052628.1
COORDINATES: similar to AA sequence:RefSeq:WP_001312821.1
COORDINATES: similar to AA sequence:RefSeq:WP_001532579.1
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_001307279.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015065592.1
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:NF013152.2
COORDINATES: protein motif:HMM:NF027409.2
COORDINATES: similar to AA sequence:RefSeq:WP_001293470.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612087.1
COORDINATES: protein motif:HMM:NF023351.2
inverse autotransporter beta-barrel domain-containing protein