Sphingomonas changnyeongensis strain C33 plasmid pC33, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Sphingomonas changnyeongensis sp. nov. isolated from the Hapcheon-Changnyeong barrage area in the Nakdong river
Submitted (15-JAN-2020) Environmental Science & Ecological Engineering., Korea University, Seoungbuk-Gu Anam-Ro 145, Seoul 20841, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP047896.1.\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 Method :: HGAP v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 243.75x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/13/2022 08:22:57\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,963\nCDSs (total) :: 2,907\nGenes (coding) :: 2,675\nCDSs (with protein) :: 2,675\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 232\nCDSs (without protein) :: 232\nPseudo Genes (ambiguous residues) :: 0 of 232\nPseudo Genes (frameshifted) :: 197 of 232\nPseudo Genes (incomplete) :: 45 of 232\nPseudo Genes (internal stop) :: 8 of 232\nPseudo Genes (multiple problems) :: 17 of 232\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingomonas changnyeongensis
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF019335.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
TonB-dependent receptor plug domain-containing protein
COORDINATES: protein motif:HMM:TIGR01782.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010546363.1
COORDINATES: similar to AA sequence:RefSeq:WP_010546364.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517424.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611976.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025024.2
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_019515156.1
COORDINATES: similar to AA sequence:RefSeq:WP_013210487.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
prolyl oligopeptidase family serine peptidase
COORDINATES: similar to AA sequence:RefSeq:WP_018533808.1
Tat pathway signal sequence domain protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611490.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017977383.1
COORDINATES: similar to AA sequence:RefSeq:WP_017167304.1
LytTR family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007674528.1
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015496024.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611305.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010913642.1
COORDINATES: similar to AA sequence:RefSeq:WP_008946277.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611843.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_007163752.1
COORDINATES: similar to AA sequence:RefSeq:WP_010126803.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930604.1
COORDINATES: similar to AA sequence:RefSeq:WP_016393522.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831361.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831362.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076611975.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF027249.2
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018387547.1
internal stop; 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_018096497.1
COORDINATES: protein motif:HMM:NF037405.2
COORDINATES: protein motif:HMM:NF024593.2
COORDINATES: similar to AA sequence:RefSeq:WP_017184057.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611444.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_013845520.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024118.2
COORDINATES: protein motif:HMM:NF025053.2
protein phosphatase 2C domain-containing protein
COORDINATES: protein motif:HMM:NF025054.2
COORDINATES: protein motif:HMM:NF025471.2
COORDINATES: similar to AA sequence:RefSeq:WP_019368397.1
COORDINATES: similar to AA sequence:RefSeq:WP_009026004.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_010336525.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_008561232.1
TM0106 family RecB-like putative nuclease
COORDINATES: similar to AA sequence:RefSeq:WP_008534080.1
COORDINATES: similar to AA sequence:RefSeq:WP_015459600.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823120.1
COORDINATES: similar to AA sequence:RefSeq:WP_010161574.1
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015459204.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688255.1
COORDINATES: similar to AA sequence:RefSeq:WP_011444010.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_009025960.1
COORDINATES: protein motif:HMM:NF013601.2
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF013395.2
COORDINATES: protein motif:HMM:NF021508.2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010165429.1
COORDINATES: similar to AA sequence:RefSeq:WP_018062309.1
RHS repeat-associated core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003819590.1
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF016701.2
COORDINATES: similar to AA sequence:RefSeq:WP_017671805.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390217.1
COORDINATES: protein motif:HMM:NF035944.1
PEPxxWA-CTERM sorting domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010544511.1
COORDINATES: similar to AA sequence:RefSeq:WP_008072073.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008603927.1
COORDINATES: protein motif:HMM:NF012546.2
COORDINATES: protein motif:HMM:NF016296.2
COORDINATES: similar to AA sequence:RefSeq:WP_005665864.1
bifunctional helix-turn-helix transcriptional regulator/GNAT family N-acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_007686311.1
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818215.1