Sphingobium cloacae strain JCM 10874 plasmid pSCLO_4, 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\nAP017658.1.\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_007688084.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017183652.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_015449221.1
COORDINATES: similar to AA sequence:RefSeq:WP_013041559.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686501.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820505.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element IS6100 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_007683476.1
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_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_007406232.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406247.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165392.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950391.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213211.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039114.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_013039065.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039064.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_018116989.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611673.1
COORDINATES: similar to AA sequence:RefSeq:WP_009489085.1
COORDINATES: protein motif:HMM:NF019845.2
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611857.1
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.
helix-turn-helix domain-containing protein
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: similar to AA sequence:RefSeq:WP_076611538.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_076611856.1
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: similar to AA sequence:RefSeq:WP_012881183.1
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_015063480.1
COORDINATES: protein motif:HMM:NF016144.2
COORDINATES: similar to AA sequence:RefSeq:WP_012755369.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054269.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
COORDINATES: protein motif:HMM:NF025120.2
COORDINATES: similar to AA sequence:RefSeq:WP_013651621.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018412614.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686149.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686150.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
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.; 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:WP_007568457.1
COORDINATES: similar to AA sequence:RefSeq:WP_006956727.1
COORDINATES: similar to AA sequence:RefSeq:WP_013635002.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849887.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501669.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015734.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251322.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_008830763.1
COORDINATES: similar to AA sequence:RefSeq:WP_006611549.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251386.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830766.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950672.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950671.1
COORDINATES: similar to AA sequence:RefSeq:WP_020817906.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683419.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683421.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683423.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011631886.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683426.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039051.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849905.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039047.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849903.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017182164.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_013041153.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054566.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688045.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039043.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688055.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849899.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744705.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849897.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849896.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744708.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849894.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688068.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688069.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688070.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013849893.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_016744714.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007688073.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020820500.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124876.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007688077.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007688079.1
COORDINATES: similar to AA sequence:RefSeq:WP_013041753.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688081.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824075.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183650.1