Sphingobium cloacae strain JCM 10874 plasmid pSCLO_6.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingobium.
Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T
Submitted (04-OCT-2016) 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\nAP017660.1.\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 :: FALCON v. 0.2.1\nGenome Coverage :: 382x\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 02:22:01\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) :: 4,611\nCDSs (total) :: 4,552\nGenes (coding) :: 4,390\nCDSs (with protein) :: 4,390\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 162\nCDSs (without protein) :: 162\nPseudo Genes (ambiguous residues) :: 0 of 162\nPseudo Genes (frameshifted) :: 61 of 162\nPseudo Genes (incomplete) :: 120 of 162\nPseudo Genes (internal stop) :: 14 of 162\nPseudo Genes (multiple problems) :: 28 of 162\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_007686160.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004213319.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686157.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686155.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686152.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000904895.1
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_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442269.1
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017501681.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832586.1
COORDINATES: similar to AA sequence:RefSeq:WP_013041578.1
COORDINATES: similar to AA sequence:RefSeq:WP_012554518.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831324.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503755.1
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_007685988.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007685989.1
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013038659.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831326.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503387.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831328.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213387.1
COORDINATES: similar to AA sequence:RefSeq:WP_015918564.1
COORDINATES: protein motif:HMM:NF012312.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
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
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
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: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:NF016176.2
COORDINATES: similar to AA sequence:RefSeq:WP_012321321.1
COORDINATES: similar to AA sequence:RefSeq:WP_008833472.1
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_010339591.1
COORDINATES: similar to AA sequence:RefSeq:WP_012076428.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013831444.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
IS6-like element IS6100 family transposase
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_018075411.1
GO:0004620 - phospholipase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007686165.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449240.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_007686162.1