Sphingomonas bisphenolicum strain AO1 plasmid pBAR1, 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\nAP018819.1.\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: similar to AA sequence:RefSeq:WP_006961814.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017184089.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012806830.1
COORDINATES: similar to AA sequence:RefSeq:WP_006964400.1
COORDINATES: similar to AA sequence:RefSeq:WP_017161247.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053952.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_006964394.1
COORDINATES: similar to AA sequence:RefSeq:WP_006964392.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: protein motif:HMM:NF018934.2
GO:0042834 - peptidoglycan binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006964383.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053955.1
P-type conjugative transfer protein TrbJ
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012478193.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_006964375.1
IncP-type conjugative transfer protein TrbN
COORDINATES: similar to AA sequence:RefSeq:WP_013041567.1
COORDINATES: similar to AA sequence:RefSeq:WP_013041566.1
COORDINATES: similar to AA sequence:RefSeq:WP_006964370.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013041565.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS6-like element IS6100 family transposase
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012296.2
COORDINATES: similar to AA sequence:RefSeq:WP_006833790.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008929952.1
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_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184087.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954207.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014579469.1
COORDINATES: similar to AA sequence:RefSeq:WP_020308529.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184081.1
COORDINATES: similar to AA sequence:RefSeq:WP_020485815.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954197.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954195.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_019053941.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053940.1
COORDINATES: similar to AA sequence:RefSeq:WP_017161207.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954189.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655356.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006954186.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_006954185.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005221527.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954183.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_006954178.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954176.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053930.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954175.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053929.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954173.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954172.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_011090936.1
COORDINATES: similar to AA sequence:RefSeq:WP_006956108.1
COORDINATES: similar to AA sequence:RefSeq:WP_011533568.1
COORDINATES: protein motif:HMM:NF017050.2
GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017181641.1
COORDINATES: similar to AA sequence:RefSeq:WP_010337432.1
GO:0018659 - 4-hydroxybenzoate 3-monooxygenase activity [Evidence IEA]
GO:0018874 - benzoate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007708652.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024701.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF013698.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF015043.2
COORDINATES: similar to AA sequence:RefSeq:WP_013837213.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008840092.1
COORDINATES: similar to AA sequence:RefSeq:WP_015932812.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_011445512.1
Tm-1-like ATP-binding domain-containing protein
COORDINATES: protein motif:HMM:NF005457.0
GO:0009317 - acetyl-CoA carboxylase complex [Evidence IEA]
GO:0003989 - acetyl-CoA carboxylase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009154773.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
biotin carboxylase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011445509.1
COORDINATES: protein motif:HMM:NF024740.2
COORDINATES: protein motif:HMM:NF013676.2