Sphingobium amiense strain DSM 16289 plasmid pSAMIE_2, 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\nAP018665.1.\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_011906626.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010890895.1
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_007015948.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054306.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_010124636.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339854.1
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_007184077.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012430576.1
4-oxalocrotonate tautomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611978.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611646.1
frameshifted; internal stop; 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_076612218.1
GO:0004803 - transposase activity [Evidence IEA]
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: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
COORDINATES: similar to AA sequence:RefSeq:WP_019052518.1
COORDINATES: similar to AA sequence:RefSeq:WP_010338396.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014077229.1
COORDINATES: protein motif:HMM:NF014385.2
COORDINATES: similar to AA sequence:RefSeq:WP_013039223.1
IS1380-like element ISSp1 family transposase
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: protein motif:HMM:NF012335.2
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_013041572.1
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_011051576.1
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_020817759.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183076.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460617.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460618.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961814.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
COORDINATES: protein motif:HMM:NF013180.2
COORDINATES: similar to AA sequence:RefSeq:WP_008829917.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829918.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829919.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829920.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829921.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829922.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_020818487.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020818486.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011413799.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503360.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818484.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829929.1
COORDINATES: similar to AA sequence:RefSeq:WP_010544136.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829931.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010186134.1
COORDINATES: protein motif:HMM:NF018894.2
COORDINATES: similar to AA sequence:RefSeq:WP_008829936.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950651.1
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_008829940.1
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_017980375.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829942.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008829943.1
GO:0004612 - phosphoenolpyruvate carboxykinase (ATP) activity [Evidence IEA]
GO:0006094 - gluconeogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829944.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829946.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950645.1
GO:0000036 - acyl carrier activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829948.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829949.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950643.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054277.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015600.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950641.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829954.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339773.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829956.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829957.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_015460511.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_011950635.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829960.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_011950633.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950632.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829963.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818502.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950629.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829966.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054292.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950626.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_011950625.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_015460523.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_010339789.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950622.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832023.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818513.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832021.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950617.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_012976033.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650732.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012048460.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_017502970.1
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_017502971.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017502972.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010338400.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010920760.1
GO:0009055 - electron transfer activity [Evidence IEA]
cytochrome b/b6 domain-containing protein
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013039775.1
COORDINATES: protein motif:HMM:NF021623.2
COORDINATES: protein motif:HMM:NF024039.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019473.2
limonene-1,2-epoxide hydrolase family protein
COORDINATES: protein motif:HMM:NF015582.2
cytochrome C oxidase subunit IV family protein
COORDINATES: protein motif:HMM:NF012334.2
COORDINATES: similar to AA sequence:RefSeq:WP_004863096.1
COORDINATES: similar to AA sequence:RefSeq:WP_017672378.1
COORDINATES: protein motif:HMM:NF012720.2
COORDINATES: similar to AA sequence:RefSeq:WP_008829910.1
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007683855.1
GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
GO:0022900 - electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829908.1
COORDINATES: similar to AA sequence:RefSeq:WP_014076995.1
COORDINATES: similar to AA sequence:RefSeq:WP_008993540.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_008829904.1
GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829893.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124788.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829891.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950480.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950481.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017182696.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950483.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831362.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829885.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950485.1
GO:0005515 - protein binding [Evidence IEA]
HWE histidine kinase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950486.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829882.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405773.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829880.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054787.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829878.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008829877.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829876.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460600.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829874.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829873.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950494.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829871.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950497.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829869.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183728.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950500.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460589.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831352.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950504.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831350.1
COORDINATES: similar to AA sequence:RefSeq:WP_019370856.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950507.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950508.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832498.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832497.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832496.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008832495.1
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008829640.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950516.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015525.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015524.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819454.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015522.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819452.1
COORDINATES: similar to AA sequence:RefSeq:WP_007013294.1
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011342702.1
COORDINATES: similar to AA sequence:RefSeq:WP_010335516.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819448.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501048.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054419.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250446.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124616.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950461.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339712.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054429.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054428.1
COORDINATES: similar to AA sequence:RefSeq:WP_013846912.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339708.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950466.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819415.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015493.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339704.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953714.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405807.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015483.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039035.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039034.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578687.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039032.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405810.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010124624.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405815.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015827.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408889.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831884.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015940.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212846.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449381.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831566.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124626.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950794.1