Rhizorhabdus dicambivorans strain Ndbn-20 plasmid p1, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Rhizorhabdus.
A Tetrahydrofolate-Dependent Methyltransferase Catalyzing the Demethylation of Dicamba in Sphingomonas sp. Strain Ndbn-20
Submitted (17-SEP-2017) College of Life Science, Nanjing Agricultural University, Number 6 of Tongwei Road, Nanjing, Jiangsu 210000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP023450.1.\nBacteria and source DNA available from culture-collection.\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 :: HGAP_Assembly v. SMRT Analysis 2.3.0\nExpected Final Version :: yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Single Molecule, Real-Time\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/19/2022 13:40:06\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) :: 5,308\nCDSs (total) :: 5,250\nGenes (coding) :: 5,152\nCDSs (with protein) :: 5,152\nGenes (RNA) :: 58\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 98\nCDSs (without protein) :: 98\nPseudo Genes (ambiguous residues) :: 0 of 98\nPseudo Genes (frameshifted) :: 50 of 98\nPseudo Genes (incomplete) :: 64 of 98\nPseudo Genes (internal stop) :: 7 of 98\nPseudo Genes (multiple problems) :: 21 of 98\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Rhizorhabdus dicambivorans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020486668.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007406428.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542818.1
COORDINATES: protein motif:HMM:NF014385.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
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_010124864.1
GO:0005215 - transporter activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018251208.1
COORDINATES: similar to AA sequence:RefSeq:WP_012522010.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542828.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542829.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019929020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542831.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
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_008068555.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542834.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018867921.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015637.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542838.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542839.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542840.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011542842.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011542848.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744747.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542850.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542851.1
COORDINATES: protein motif:HMM:NF022072.2
COORDINATES: similar to AA sequence:RefSeq:WP_011542853.1
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_011542855.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011542856.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015414.1
COORDINATES: similar to AA sequence:RefSeq:WP_012384997.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834345.1
CDF family Co(II)/Ni(II) efflux transporter DmeF
COORDINATES: similar to AA sequence:RefSeq:WP_014718626.1
metal/formaldehyde-sensitive transcriptional repressor
COORDINATES: similar to AA sequence:RefSeq:WP_009824046.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012649577.1
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
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
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: similar to AA sequence:RefSeq:WP_007688079.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744725.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818725.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017183284.1
COORDINATES: similar to AA sequence:RefSeq:WP_008068559.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818728.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012521999.1
ArsI/CadI family heavy metal resistance metalloenzyme
COORDINATES: similar to AA sequence:RefSeq:WP_004619506.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010405484.1
COORDINATES: similar to AA sequence:RefSeq:WP_015459658.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017183281.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124876.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_020820500.1
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_016744714.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849893.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_007688070.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007688069.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688068.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849894.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744708.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849896.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849897.1
COORDINATES: similar to AA sequence:RefSeq:WP_012510977.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004212800.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_007688059.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849899.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688055.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039043.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688045.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039045.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_013849903.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039047.1
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039051.1
COORDINATES: similar to AA sequence:RefSeq:WP_017499939.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339384.1
COORDINATES: similar to AA sequence:RefSeq:WP_012050248.1
COORDINATES: similar to AA sequence:RefSeq:WP_017499942.1
COORDINATES: similar to AA sequence:RefSeq:WP_017499943.1
COORDINATES: similar to AA sequence:RefSeq:WP_017499944.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039058.1
nucleoside triphosphate pyrophosphohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017499946.1
COORDINATES: similar to AA sequence:RefSeq:WP_016743835.1
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_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_013849913.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039064.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_013039065.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683405.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683402.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683400.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_015449339.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039070.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039071.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039072.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039073.1
phytanoyl-CoA dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007683387.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449333.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849920.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212754.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683381.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039078.1
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_009823969.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503361.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683376.1
response regulator for histidine kinase FixL; part of global network that controls expression of aerobic respiratory terminal oxidases and carbon and nitrogen metabolic enzymes; 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_008994784.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994783.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
COORDINATES: similar to AA sequence:RefSeq:WP_003495445.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_010405610.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
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_010126951.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010405980.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406406.1
PAS domain-containing sensor histidine kinase
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_011199097.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961814.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501291.1
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_004212674.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406401.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212666.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449267.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007406411.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406380.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824015.1
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_007406382.1
COORDINATES: similar to AA sequence:RefSeq:WP_010126928.1
heavy metal-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012286362.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212653.1