Rhizorhabdus dicambivorans strain Ndbn-20 plasmid p3, 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\nCP023452.1.\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: similar to AA sequence:RefSeq:WP_008932199.1
GO:0008270 - zinc ion binding [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012791.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013868.2
COORDINATES: protein motif:HMM:NF013109.2
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF03058
sul1 is cis-regulatory element that is thought to sense ions involved in sulfur or methionine metabolism; They are found in Alphaproteobacteria; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006953891.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_036759113.1
COORDINATES: similar to AA sequence:RefSeq:WP_032490499.1
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_004213313.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054017.1
COORDINATES: similar to AA sequence:RefSeq:WP_006968047.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213405.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020819819.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949645.1
COORDINATES: protein motif:HMM:NF019542.2
COORDINATES: similar to AA sequence:RefSeq:WP_003603269.1
COORDINATES: protein motif:HMM:NF033572.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819817.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016055.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819815.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213195.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213200.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213202.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949650.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213205.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_006949655.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949657.1
COORDINATES: similar to AA sequence:RefSeq:WP_011627750.1
COORDINATES: protein motif:HMM:NF038091.1
COORDINATES: similar to AA sequence:RefSeq:WP_011627746.1
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_020819805.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213228.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213229.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953926.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213271.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213273.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_006953923.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213275.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213276.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213277.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213279.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF016432.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma factor-like helix-turn-helix DNA-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013054029.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017503334.1