Sphingobium cloacae strain JCM 10874 plasmid pSCLO_3, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingobium.
Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T
Submitted (04-OCT-2016) Contact:Tomoyasu Nishizawa Ibaraki University College of Agriculture, Department of Bioresource sience; 3-21-1 Chuou, Ami, Ibaraki 300-0393, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP017657.1.\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 :: FALCON v. 0.2.1\nGenome Coverage :: 382x\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 02:22:01\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) :: 4,611\nCDSs (total) :: 4,552\nGenes (coding) :: 4,390\nCDSs (with protein) :: 4,390\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 162\nCDSs (without protein) :: 162\nPseudo Genes (ambiguous residues) :: 0 of 162\nPseudo Genes (frameshifted) :: 61 of 162\nPseudo Genes (incomplete) :: 120 of 162\nPseudo Genes (internal stop) :: 14 of 162\nPseudo Genes (multiple problems) :: 28 of 162\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_015460581.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015460580.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_015460579.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954005.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460577.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460576.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004167229.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054303.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012109885.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [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_009149913.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element IS6100 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_007686150.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_020817757.1
toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_014449488.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_020817759.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165392.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503521.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503520.1
COORDINATES: similar to AA sequence:RefSeq:WP_012975307.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961814.1
internal stop; 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: similar to AA sequence:RefSeq:WP_017501678.1
COORDINATES: similar to AA sequence:RefSeq:WP_013038674.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449240.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_020820064.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020820063.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686165.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849886.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339830.1
COORDINATES: protein motif:HMM:TIGR02783.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_017161542.1
COORDINATES: protein motif:HMM:NF015487.2
P-type conjugative transfer protein TrbG
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_017167677.1
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_008260487.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820593.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
flagellar hook-basal body complex protein FliE
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_018251229.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213304.1
COORDINATES: similar to AA sequence:RefSeq:WP_008878340.1
COORDINATES: similar to AA sequence:RefSeq:WP_012561204.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010127314.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_010127316.1
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_016744747.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
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_008828956.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828955.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820596.1
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_007568958.1
COORDINATES: similar to AA sequence:RefSeq:WP_013786598.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010189087.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831131.1
COORDINATES: protein motif:HMM:NF025034.2
COORDINATES: similar to AA sequence:RefSeq:WP_013039223.1
IS1380-like element ISSp1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_013849884.1
COORDINATES: similar to AA sequence:RefSeq:WP_010127339.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092685.1
COORDINATES: similar to AA sequence:RefSeq:WP_019086523.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212886.1
COORDINATES: similar to AA sequence:RefSeq:WP_010185698.1
COORDINATES: similar to AA sequence:RefSeq:WP_012495579.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212882.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820603.1
COORDINATES: similar to AA sequence:RefSeq:WP_007630324.1
COORDINATES: similar to AA sequence:RefSeq:WP_003949419.1
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: protein motif:HMM:NF019845.2
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: protein motif:HMM:NF004829.0
bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612218.1
COORDINATES: protein motif:HMM:NF017528.2
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: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF012720.2
COORDINATES: protein motif:HMM:NF015582.2
cytochrome C oxidase subunit IV family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017672378.1
COORDINATES: similar to AA sequence:RefSeq:WP_004863096.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019473.2
limonene-1,2-epoxide hydrolase family protein
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]
COORDINATES: similar to AA sequence:RefSeq:WP_043766072.1
COORDINATES: similar to AA sequence:RefSeq:WP_011608154.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212934.1
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_016918838.1
COORDINATES: similar to AA sequence:RefSeq:WP_015063472.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212937.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114071.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018308607.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011408759.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818513.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406719.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015460525.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339790.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339789.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460523.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_006953591.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_007406605.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_007015613.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460519.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460518.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818502.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502436.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460515.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_010124755.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015607.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_011950635.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460511.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_015460510.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_007015603.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460508.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054653.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015600.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017184762.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820449.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818487.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020818486.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008829925.1
COORDINATES: similar to AA sequence:RefSeq:WP_010910886.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829927.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828317.1
COORDINATES: similar to AA sequence:RefSeq:WP_004209664.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184756.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183347.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818773.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829340.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006952559.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405773.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054788.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054787.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950430.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_021234579.1
COORDINATES: protein motif:HMM:NF012307.2
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015484.1
COORDINATES: similar to AA sequence:RefSeq:WP_006392129.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054348.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020819396.1
COORDINATES: similar to AA sequence:RefSeq:WP_020297366.1
COORDINATES: protein motif:HMM:NF014573.2
COORDINATES: protein motif:HMM:NF024258.2
COORDINATES: similar to AA sequence:RefSeq:WP_007683421.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503640.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503639.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831019.1