Novosphingobium pentaromativorans US6-1 plasmid pLA2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium.
Complete genome sequence of Novosphingobium pentaromativorans US6-1(T)
Submitted (28-AUG-2014) Marine Biotechnology, KIOST, 787, Haeanro, Ansan, Gyeonggi-do 426-744, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP009296.1.\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 Date :: 26-MAY-2014\nAssembly Method :: Roche gs Assembler v. 2.6; PAC Bio SMRT\n Analysis v. 2.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 128.0x\nSequencing Technology :: Illumina MiSeq; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 00:17:37\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) :: 5,173\nCDSs (total) :: 5,106\nGenes (coding) :: 5,011\nCDSs (with protein) :: 5,011\nGenes (RNA) :: 67\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 95\nCDSs (without protein) :: 95\nPseudo Genes (ambiguous residues) :: 0 of 95\nPseudo Genes (frameshifted) :: 38 of 95\nPseudo Genes (incomplete) :: 69 of 95\nPseudo Genes (internal stop) :: 15 of 95\nPseudo Genes (multiple problems) :: 22 of 95\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Novosphingobium pentaromativorans
COORDINATES: similar to AA sequence:RefSeq:WP_006953921.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006953923.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213273.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_004213271.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006953926.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016080.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072605.1
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_004213269.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014072607.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213267.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213266.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213265.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072611.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007016074.1
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213260.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016073.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019706040.1
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_006967586.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007016061.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015726.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006967582.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_076611221.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017183626.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015723.1
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_004213229.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213228.1
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_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_004213224.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949660.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213217.1
COORDINATES: similar to AA sequence:RefSeq:WP_011627750.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949657.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949655.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213205.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_006949650.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213202.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213200.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213195.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819815.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213191.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819817.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949645.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819819.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213405.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006968047.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054017.1
COORDINATES: protein motif:HMM:NF024013.2
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213313.1
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_006953883.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213311.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213310.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054019.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953889.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953891.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953895.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953897.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054022.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054023.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831892.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819825.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213291.1
COORDINATES: similar to AA sequence:RefSeq:WP_008827849.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503334.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054029.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006953917.1
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_004213279.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213277.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213276.1