Sphingomonas bisphenolicum strain AO1 plasmid pBAR2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Complete genome sequence of Sphingomonas bisphenolicum strain AO1, a bisphenol A degradative bacterium isolated from Japanese farm field
Submitted (25-JUL-2018) Contact:Yoshinobu Matsumura Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University; Yamatecho 3-3-35, Suita, Osaka 564-8680, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP018820.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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 :: CLC Genomics Workbench v. 9.5.3; HGAP v. 3\nGenome Coverage :: 82x\nSequencing Technology :: illumina Miseq; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/29/2022 14:27:55\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;\n repeat_region\nGenes (total) :: 5,038\nCDSs (total) :: 4,967\nGenes (coding) :: 4,877\nCDSs (with protein) :: 4,877\nGenes (RNA) :: 71\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 59\nncRNAs :: 3\nPseudo Genes (total) :: 90\nCDSs (without protein) :: 90\nPseudo Genes (ambiguous residues) :: 0 of 90\nPseudo Genes (frameshifted) :: 40 of 90\nPseudo Genes (incomplete) :: 52 of 90\nPseudo Genes (internal stop) :: 5 of 90\nPseudo Genes (multiple problems) :: 6 of 90\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingomonas bisphenolicum
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0016491 - oxidoreductase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF025607.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025878.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012596.2
enoyl-CoA hydratase/isomerase family protein
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF036525.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013039223.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013039791.1
COORDINATES: similar to AA sequence:RefSeq:WP_006159514.1
COORDINATES: similar to AA sequence:RefSeq:WP_008905427.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013501458.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965234.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980757.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502412.1
COORDINATES: similar to AA sequence:RefSeq:WP_009209116.1
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_076611716.1
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_010442269.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
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_013041578.1
COORDINATES: similar to AA sequence:RefSeq:WP_012554518.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831324.1
COORDINATES: similar to AA sequence:RefSeq:WP_014003226.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013521176.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004213387.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212934.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013041572.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818519.1
COORDINATES: similar to AA sequence:RefSeq:WP_012048821.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039111.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
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_019054269.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054268.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339226.1
COORDINATES: similar to AA sequence:RefSeq:WP_007685988.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503755.1
COORDINATES: similar to AA sequence:RefSeq:WP_013038655.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004213364.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213365.1
COORDINATES: similar to AA sequence:RefSeq:WP_010511350.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501681.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832942.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010336374.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213210.1
COORDINATES: similar to AA sequence:RefSeq:WP_012975307.1
COORDINATES: similar to AA sequence:RefSeq:WP_013038680.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213318.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449236.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213321.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686162.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831346.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_010339209.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339208.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501674.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184065.1
COORDINATES: protein motif:HMM:NF016430.2
COORDINATES: similar to AA sequence:RefSeq:WP_013849887.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501669.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF013676.2
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008305448.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein