Sphingopyxis macrogoltabida strain 203 plasmid unnamed, complete sequence.
Sphingopyxis macrogoltabida (Sphingomonas macrogoltabidus)
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingopyxis.
Complete genome sequence of a mutant derivative (NBRC15033) of polyethylene glycol-degrading strain Sphingopyxis macrogoltabidus strain 203
Submitted (05-OCT-2015) Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Sendai, Miyagi 980-8577, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nCP009431.1.\nWhole genome shotgun sequencing was performed at NITE. Finishing\nwas conducted at Tohoku University with the aid of GenoFinisher,\nAceFileViewer, and ShortReadManager software\n(http://www.ige.tohoku.ac.jp/joho/gf_e/index.php). Autoannotation\nwas conducted using PGAP and MiGAP, and PGAP annotation was curated\nby referencing to the MiGAP annotation with the aid of annotation\nsupport tool of GenomeMatcher software. Strain 203 is available\nfrom NBRC culture collection (http://www.nbrc.nite.go.jp/e/).\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 :: Newbler v. 2.8\nGenome Coverage :: 60x\nSequencing Technology :: Illumina HiSeq; 454 Titanium\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 19:36:47\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) :: 5,623\nCDSs (total) :: 5,560\nGenes (coding) :: 5,488\nCDSs (with protein) :: 5,488\nGenes (RNA) :: 63\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 57\nncRNAs :: 3\nPseudo Genes (total) :: 72\nCDSs (without protein) :: 72\nPseudo Genes (ambiguous residues) :: 0 of 72\nPseudo Genes (frameshifted) :: 24 of 72\nPseudo Genes (incomplete) :: 53 of 72\nPseudo Genes (internal stop) :: 5 of 72\nPseudo Genes (multiple problems) :: 9 of 72\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingopyxis macrogoltabida
COORDINATES: similar to AA sequence:RefSeq:WP_007682384.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009824073.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824071.1
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_006949334.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820384.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405731.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405730.1
COORDINATES: similar to AA sequence:RefSeq:WP_011793847.1
COORDINATES: protein motif:HMM:NF012307.2
COORDINATES: protein motif:HMM:NF018430.2
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
IS256-like element ISSpma2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_010234285.1
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007164754.1
COORDINATES: protein motif:HMM:NF028240.2
COORDINATES: similar to AA sequence:RefSeq:WP_006473457.1
IS1380-like element IS1247 family transposase
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010339860.1
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010408871.1
COORDINATES: protein motif:HMM:NF015393.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007685341.1
COORDINATES: similar to AA sequence:RefSeq:WP_008065174.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_011950625.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_007685336.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_007685334.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460519.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818502.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831568.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_007685322.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054285.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_019054283.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_007685310.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_015460508.1
COORDINATES: similar to AA sequence:RefSeq:WP_007685301.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683193.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003630695.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831992.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831993.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: protein motif:HMM:NF014035.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007686149.1
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_020485769.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_020678642.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_010543588.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188646.1
COORDINATES: protein motif:HMM:NF016701.2
GO:0016846 - carbon-sulfur lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019054176.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054175.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054174.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241803.1
COORDINATES: similar to AA sequence:RefSeq:WP_003571788.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054171.1
COORDINATES: similar to AA sequence:RefSeq:WP_010337663.1
COORDINATES: similar to AA sequence:RefSeq:WP_017500318.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_013849199.1
PepSY-associated TM helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017172645.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008603797.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251372.1
COORDINATES: similar to AA sequence:RefSeq:WP_010661771.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017184236.1
COORDINATES: similar to AA sequence:RefSeq:WP_011518379.1
COORDINATES: similar to AA sequence:RefSeq:WP_007220500.1
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: similar to AA sequence:RefSeq:WP_017184237.1
COORDINATES: protein motif:HMM:NF033816.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013481237.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831994.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003630700.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518567.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518566.1
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015459676.1
COORDINATES: protein motif:HMM:NF024835.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006952696.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686605.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686607.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013561.2
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011413111.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950494.1
COORDINATES: protein motif:HMM:NF036894.2
COORDINATES: similar to AA sequence:RefSeq:WP_007688513.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820333.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010890929.1
COORDINATES: protein motif:HMM:NF017128.2
COORDINATES: similar to AA sequence:RefSeq:WP_006953773.1
COORDINATES: similar to AA sequence:RefSeq:WP_008068549.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688483.1
COORDINATES: similar to AA sequence:RefSeq:WP_017671805.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390217.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953712.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015483.1
COORDINATES: protein motif:HMM:NF014273.2
COORDINATES: similar to AA sequence:RefSeq:WP_018481099.1
COORDINATES: similar to AA sequence:RefSeq:WP_018481098.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007688471.1