Tardibacter chloracetimidivorans strain JJ-A5 plasmid pHSL4, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Tardibacter.
Complete Genome Sequence of alachlor-degrading Sphingomonas sp. strain JJ-A5
Submitted (29-NOV-2016) Department of Applied Biology and Chemistry, College of Agriculture and Life Science, Seoul National University, San 56-1, Sillimdong, Gwanakgu, Seoul 151-742, Republic of Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP018225.1.\nBacteria and source DNA available from Environmental Microbiology\nLaboratory, Department of Agricultural Biotechnology and Research\nInstitute of Agriculture and Life Sciences, Seoul National\nUniversity, Seoul 151-742, Republic of Korea.\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 Date :: 21-OCT-2016\nAssembly Method :: celera assembler v. Oct-2016\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 215.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 02:51:27\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) :: 3,995\nCDSs (total) :: 3,944\nGenes (coding) :: 3,864\nCDSs (with protein) :: 3,864\nGenes (RNA) :: 51\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 1\nPseudo Genes (total) :: 80\nCDSs (without protein) :: 80\nPseudo Genes (ambiguous residues) :: 0 of 80\nPseudo Genes (frameshifted) :: 21 of 80\nPseudo Genes (incomplete) :: 68 of 80\nPseudo Genes (internal stop) :: 5 of 80\nPseudo Genes (multiple problems) :: 12 of 80\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type material of Tardibacter chloracetimidivorans Lee et al. 2018
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611893.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009823943.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015449381.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832422.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015940.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824076.1
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
COORDINATES: similar to AA sequence:RefSeq:WP_007688084.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183652.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449221.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_009824068.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824067.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649577.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824046.1
COORDINATES: similar to AA sequence:RefSeq:WP_014718626.1
metal/formaldehyde-sensitive transcriptional repressor
COORDINATES: similar to AA sequence:RefSeq:WP_013834345.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
CDF family Co(II)/Ni(II) efflux transporter DmeF
COORDINATES: similar to AA sequence:RefSeq:WP_012384997.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007015414.1
COORDINATES: protein motif:HMM:NF022072.2
COORDINATES: similar to AA sequence:RefSeq:WP_011542856.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542855.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011542854.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011542853.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542851.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542850.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_016744747.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011542848.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611117.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542842.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011542840.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542839.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542838.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015637.1
COORDINATES: similar to AA sequence:RefSeq:WP_018867921.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_011542834.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008068555.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011542832.1
GO:0033573 - high-affinity iron permease complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005381 - iron ion transmembrane transporter activity [Evidence IEA]
GO:0034755 - iron ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011542831.1
COORDINATES: similar to AA sequence:RefSeq:WP_019929020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542829.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542828.1
COORDINATES: similar to AA sequence:RefSeq:WP_012522010.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251208.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124864.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124863.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542818.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406428.1
COORDINATES: similar to AA sequence:RefSeq:WP_020486668.1
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_012286362.1
COORDINATES: similar to AA sequence:RefSeq:WP_010126928.1
heavy metal-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007406382.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824016.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824015.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406380.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406411.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449267.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004212666.1
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_007406401.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212674.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501291.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683342.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212677.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_009823975.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683345.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017501296.1
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_004212690.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011608154.1
frameshifted; 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_043766072.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_004212696.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212697.1
COORDINATES: similar to AA sequence:RefSeq:WP_008121551.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212701.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683808.1
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_015449321.1
COORDINATES: protein motif:HMM:NF015669.2
COORDINATES: similar to AA sequence:RefSeq:WP_004212708.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
cytochrome-c oxidase, cbb3-type subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_004212709.1
cytochrome-c oxidase, cbb3-type subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_018009698.1
cbb3-type cytochrome c oxidase subunit 3
COORDINATES: similar to AA sequence:RefSeq:WP_004212713.1
cytochrome-c oxidase, cbb3-type subunit III
COORDINATES: similar to AA sequence:RefSeq:WP_008839047.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212715.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449327.1
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_076611716.1
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_020094673.1
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_003497247.1
COORDINATES: protein motif:HMM:NF015863.2
PepSY-associated TM helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016743854.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501299.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017270994.1
magnesium and cobalt transport protein CorA
COORDINATES: similar to AA sequence:RefSeq:WP_013039094.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020820519.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406406.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683361.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683363.1
GO:0005507 - copper ion binding [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013039089.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683367.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449249.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683370.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212741.1
GO:0042597 - periplasmic space [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_007406374.1
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_010336582.1
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_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_007683376.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503361.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823969.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849922.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212750.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039078.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683381.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004212754.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849920.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039074.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683387.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013039073.1
phytanoyl-CoA dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039072.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039071.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039070.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449339.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_007683400.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_007683402.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683405.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039065.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039064.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_013849913.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683413.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013039061.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015449348.1
COORDINATES: similar to AA sequence:RefSeq:WP_017499946.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039058.1
nucleoside triphosphate pyrophosphohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039057.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039056.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039055.1
COORDINATES: similar to AA sequence:RefSeq:WP_012050248.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339384.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019051867.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039051.1
COORDINATES: protein motif:HMM:NF020419.2
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_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_015449373.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818728.1
COORDINATES: similar to AA sequence:RefSeq:WP_008068559.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183284.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818725.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016744725.1
COORDINATES: similar to AA sequence:RefSeq:WP_008996396.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930444.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930445.1
ArdC-like ssDNA-binding domain-containing protein