Sphingobium cloacae strain JCM 10874 plasmid pSCLO_5, complete sequence.
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\nAP017659.1.\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##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_006954197.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006954195.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008996020.1
COORDINATES: similar to AA sequence:RefSeq:WP_003448668.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019335.2
TonB-dependent receptor plug domain-containing protein
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF024092.2
GO:0030638 - polyketide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018116989.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013833393.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_004209593.1
COORDINATES: similar to AA sequence:RefSeq:WP_011053406.1
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_009489568.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013848413.1
COORDINATES: similar to AA sequence:RefSeq:WP_013848414.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039114.1
COORDINATES: similar to AA sequence:RefSeq:WP_020817917.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950391.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165392.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406247.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406232.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213374.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007683476.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
IS6-like element IS6100 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_020820505.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686501.1
COORDINATES: similar to AA sequence:RefSeq:WP_013041559.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449221.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183652.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688084.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183650.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824075.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688081.1
COORDINATES: similar to AA sequence:RefSeq:WP_013041753.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_017501669.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
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_013635002.1
COORDINATES: similar to AA sequence:RefSeq:WP_006956727.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007568457.1
COORDINATES: similar to AA sequence:RefSeq:WP_010161711.1
DNA polymerase involved in damage-induced mutagenesis and translesion synthesis. It is not the major replicative DNA polymerase.; 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: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_007686149.1
COORDINATES: protein motif:HMM:NF013676.2
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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:WP_011408759.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651621.1
COORDINATES: protein motif:HMM:NF025120.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054269.1
COORDINATES: similar to AA sequence:RefSeq:WP_012755369.1
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: protein motif:HMM:NF016144.2