Sphingobium amiense strain DSM 16289 plasmid pSAMIE_4, 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\nAP018667.1.\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_008827689.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015472929.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000983249.1
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_006961814.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_008604018.1
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_032490240.1
COORDINATES: similar to AA sequence:RefSeq:WP_004863096.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012656.2
COORDINATES: similar to AA sequence:RefSeq:WP_010189087.1
COORDINATES: similar to AA sequence:RefSeq:WP_013786598.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007568958.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449233.1
COORDINATES: protein motif:HMM:NF014790.2
COORDINATES: protein motif:HMM:NF015582.2
cytochrome C oxidase subunit IV family protein
COORDINATES: protein motif:HMM:NF012720.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013677.2
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_076612218.1
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_015918564.1
COORDINATES: protein motif:HMM:NF012312.2
COORDINATES: similar to AA sequence:RefSeq:WP_008833340.1
COORDINATES: similar to AA sequence:RefSeq:WP_011053314.1
COORDINATES: similar to AA sequence:RefSeq:WP_020648694.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007248855.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010215008.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007405018.1
COORDINATES: similar to AA sequence:RefSeq:WP_008996022.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008996021.1
COORDINATES: similar to AA sequence:RefSeq:WP_008996020.1
COORDINATES: protein motif:HMM:NF019268.2
COORDINATES: similar to AA sequence:RefSeq:WP_014900394.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008996018.1
COORDINATES: similar to AA sequence:RefSeq:WP_006752307.1
GO:0018576 - catechol 1,2-dioxygenase activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0009712 - catechol-containing compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012575.2
COORDINATES: protein motif:HMM:NF016176.2
COORDINATES: similar to AA sequence:RefSeq:WP_012321321.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
IS6-like element IS6100 family transposase
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_013039775.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831444.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012076428.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339591.1
COORDINATES: similar to AA sequence:RefSeq:WP_006162678.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0003955 - NAD(P)H dehydrogenase (quinone) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008833472.1
COORDINATES: similar to AA sequence:RefSeq:WP_000904895.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
COORDINATES: similar to AA sequence:RefSeq:WP_016509640.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510868.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510871.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008827686.1
COORDINATES: similar to AA sequence:RefSeq:WP_010189082.1
COORDINATES: similar to AA sequence:RefSeq:WP_008827688.1