Sphingobium amiense strain DSM 16289 plasmid pSAMIE_3, 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\nAP018666.1.\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_008831241.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950523.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039032.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578687.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039034.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039035.1
zincin-like metallopeptidase domain-containing protein
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_008829631.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829632.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124620.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829634.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829635.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829636.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829637.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950517.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008829639.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819448.1
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006955904.1
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_007015524.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015525.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054422.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124614.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829640.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405793.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124609.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405791.1
COORDINATES: protein motif:HMM:NF014643.2
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010339728.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829869.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405786.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950494.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405783.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460600.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405780.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015563.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950430.1
type IV secretion system DNA-binding domain-containing protein
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_019054788.1
COORDINATES: similar to AA sequence:RefSeq:WP_014076970.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010405769.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405767.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405766.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405765.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405763.1
COORDINATES: similar to AA sequence:RefSeq:WP_010443065.1
COORDINATES: protein motif:HMM:NF025388.2
COORDINATES: similar to AA sequence:RefSeq:WP_011540744.1
COORDINATES: similar to AA sequence:RefSeq:WP_011608154.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124808.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010161916.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950801.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832194.1
COORDINATES: similar to AA sequence:RefSeq:WP_007013862.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501059.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_004210818.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004210816.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744735.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009821105.1
COORDINATES: similar to AA sequence:RefSeq:WP_014077332.1
COORDINATES: similar to AA sequence:RefSeq:WP_010543640.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014891315.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124772.1
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_007015601.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406581.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124763.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054282.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_019054283.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_017184770.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953576.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_010124755.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405693.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124751.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818502.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829965.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405687.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406582.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405683.1
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_008832025.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460525.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460526.1
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_009823646.1
COORDINATES: similar to AA sequence:RefSeq:WP_019052497.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807921.1
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_019054852.1
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_010123249.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011993020.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212750.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849922.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503370.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503361.1
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_020820519.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008261590.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0050151 - oleate hydratase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017501324.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501323.1
GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0046933 - proton-transporting ATP synthase activity, rotational mechanism [Evidence IEA]
GO:0015986 - proton motive force-driven ATP synthesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF012645.2
COORDINATES: similar to AA sequence:RefSeq:WP_010405656.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501320.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405654.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501318.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501317.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501316.1
GO:0000275 - mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) [Evidence IEA]; GO:0045262 - plasma membrane proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]; GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]
GO:0046933 - proton-transporting ATP synthase activity, rotational mechanism [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020820365.1
GO:0004318 - enoyl-[acyl-carrier-protein] reductase (NADH) activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007406370.1
GO:0008776 - acetate kinase activity [Evidence IEA]
GO:0006083 - acetate metabolic process [Evidence IEA]; GO:0006113 - fermentation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017501312.1
bifunctional enoyl-CoA hydratase/phosphate acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_007406387.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212744.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004212743.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010336582.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406374.1
GO:0006825 - copper ion transport [Evidence IEA]
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_004212741.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_007683370.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449249.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683367.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449251.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_007683363.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007683361.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406406.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039094.1
COORDINATES: similar to AA sequence:RefSeq:WP_017270994.1
GO:0015087 - cobalt ion transmembrane transporter activity [Evidence IEA]; GO:0015095 - magnesium ion transmembrane transporter activity [Evidence IEA]
GO:0006824 - cobalt ion transport [Evidence IEA]; GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017501299.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016743854.1
COORDINATES: protein motif:HMM:NF015863.2
PepSY-associated TM helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003497247.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611774.1
internal stop; 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_020094673.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611716.1
COORDINATES: similar to AA sequence:RefSeq:WP_009802060.1
GO:0008535 - respiratory chain complex IV assembly [Evidence IEA]
cbb3-type cytochrome oxidase assembly protein CcoS
COORDINATES: similar to AA sequence:RefSeq:WP_015449327.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212715.1
COORDINATES: similar to AA sequence:RefSeq:WP_008839047.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212713.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
cytochrome-c oxidase, cbb3-type subunit III
COORDINATES: similar to AA sequence:RefSeq:WP_018009698.1
cbb3-type cytochrome c oxidase subunit 3
COORDINATES: similar to AA sequence:RefSeq:WP_004212709.1
cytochrome-c oxidase, cbb3-type subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_004212708.1
cytochrome-c oxidase, cbb3-type subunit I
COORDINATES: protein motif:HMM:NF015669.2
COORDINATES: similar to AA sequence:RefSeq:WP_015449321.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818174.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0008941 - nitric oxide dioxygenase activity [Evidence IEA]; GO:0019825 - oxygen binding [Evidence IEA]
GO:0051409 - response to nitrosative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007683808.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212701.1
COORDINATES: similar to AA sequence:RefSeq:WP_008121551.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212697.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212696.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_021234579.1
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_004212690.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004212689.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017501296.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961814.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_016743858.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212677.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683342.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501291.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_019054306.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015948.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950540.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829215.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950538.1
COORDINATES: protein motif:HMM:NF016777.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950537.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950536.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0005515 - protein binding [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006508 - proteolysis [Evidence IEA]; GO:0006950 - response to stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008831021.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950533.1
COORDINATES: similar to AA sequence:RefSeq:WP_009404702.1
GO:0005515 - protein binding [Evidence IEA]
HWE histidine kinase domain-containing protein
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_011950531.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950530.1
COORDINATES: protein motif:HMM:NF021445.2
phosphatidylglycerol lysyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183336.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015940.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
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_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_008831245.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008831242.1