Sphingomonas bisphenolicum strain AO1 plasmid pBAR4, 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\nAP018822.1.\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_017502279.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010219225.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_010405508.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405505.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017502273.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405500.1
GO:0042597 - periplasmic space [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_017502271.1
GO:0016021 - integral component of membrane [Evidence IEA]
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_010405495.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502270.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368102.1
COORDINATES: similar to AA sequence:RefSeq:WP_010163445.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542814.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004212862.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649577.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961814.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124636.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_019054306.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015948.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183652.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007688084.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183650.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212853.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212851.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188936.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188937.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251158.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010165183.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165182.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165180.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950787.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950786.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849894.1
COORDINATES: similar to AA sequence:RefSeq:WP_010542917.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_008833348.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405483.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007004195.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952185.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019368255.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016744708.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849896.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950804.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744705.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950778.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950809.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688055.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950776.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503544.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212786.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006164860.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460380.1
COORDINATES: similar to AA sequence:RefSeq:WP_012566347.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830720.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950755.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950754.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830723.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950752.1
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_011950751.1
COORDINATES: similar to AA sequence:RefSeq:WP_017182755.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_013039065.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950748.1
COORDINATES: similar to AA sequence:RefSeq:WP_017182758.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015838.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
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_009823855.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831141.1
COORDINATES: similar to AA sequence:RefSeq:WP_006956108.1
COORDINATES: similar to AA sequence:RefSeq:WP_011090936.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212765.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_008831139.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_008831138.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831137.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039072.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831135.1
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950741.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368198.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820596.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212886.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008828948.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]; GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008828949.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405582.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828951.1
COORDINATES: similar to AA sequence:RefSeq:WP_010127326.1
COORDINATES: similar to AA sequence:RefSeq:WP_004210796.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828955.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828956.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828957.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_010405569.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013039111.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012048821.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124851.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007407012.1
COORDINATES: similar to AA sequence:RefSeq:WP_013833391.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011239965.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405541.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213013.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405534.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406384.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502287.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405525.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502284.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405522.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405520.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502281.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405516.1