Sphingobium amiense strain DSM 16289 plasmid pSAMIE_5, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingobium.
Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium amiense DSM 16289T
Submitted (07-MAY-2018) Contact:Tomoyasu Nishizawa Ibaraki University College of Agriculture, Department of Bioresource sience; 3-21-1 Chuou, Ami, Ibaraki 300-0393, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP018668.1.\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 :: SPAdes v. 3.10.1; Unicycler v. 0.4.0; Canu\n v. 1.5\nGenome Coverage :: 365x\nSequencing Technology :: PacBio RS II; Hiseq 2500\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/27/2022 02:02:55\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) :: 4,668\nCDSs (total) :: 4,607\nGenes (coding) :: 4,534\nCDSs (with protein) :: 4,534\nGenes (RNA) :: 61\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 3\nPseudo Genes (total) :: 73\nCDSs (without protein) :: 73\nPseudo Genes (ambiguous residues) :: 0 of 73\nPseudo Genes (frameshifted) :: 17 of 73\nPseudo Genes (incomplete) :: 60 of 73\nPseudo Genes (internal stop) :: 7 of 73\nPseudo Genes (multiple problems) :: 9 of 73\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_007406350.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015460617.1
COORDINATES: similar to AA sequence:RefSeq:WP_013394241.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165325.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213374.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213373.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686160.1
COORDINATES: similar to AA sequence:RefSeq:WP_013038674.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449240.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_015449241.1
COORDINATES: protein motif:HMM:NF019335.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
TonB-dependent receptor plug domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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_010405541.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820593.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
flagellar hook-basal body complex protein FliE
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: protein motif:HMM:NF015506.2
GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024734.2
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008830047.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013039427.1
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: protein motif:HMM:NF016236.2
COORDINATES: similar to AA sequence:RefSeq:WP_013833496.1
COORDINATES: protein motif:HMM:NF025736.2
COORDINATES: similar to AA sequence:RefSeq:WP_013292904.1
COORDINATES: protein motif:HMM:NF017238.2
COORDINATES: similar to AA sequence:RefSeq:WP_010338848.1
COORDINATES: similar to AA sequence:RefSeq:WP_015864217.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213342.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831331.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212934.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213387.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961814.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_014160816.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006954458.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007683476.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950671.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950672.1
COORDINATES: similar to AA sequence:RefSeq:WP_013038655.1