Spirosoma rhododendri strain CJU-R4 plasmid unnamed1, complete sequence.
Bacteria; Bacteroidota; Cytophagia; Cytophagales; Cytophagaceae; Spirosoma.
Submitted (17-APR-2020) Agricultural Mircrobiology Division, National Institute of Agricultural Sciences, 166 Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP051678.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: RS HGAP Assembly v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 140x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/01/2023 10:33:01\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) :: 5,176\nCDSs (total) :: 5,122\nGenes (coding) :: 4,955\nCDSs (with protein) :: 4,955\nGenes (RNA) :: 54\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 43\nncRNAs :: 2\nPseudo Genes (total) :: 167\nCDSs (without protein) :: 167\nPseudo Genes (ambiguous residues) :: 0 of 167\nPseudo Genes (frameshifted) :: 154 of 167\nPseudo Genes (incomplete) :: 12 of 167\nPseudo Genes (internal stop) :: 6 of 167\nPseudo Genes (multiple problems) :: 5 of 167\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0008236 - serine-type peptidase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_012927296.1
COORDINATES: similar to AA sequence:RefSeq:WP_012927295.1
COORDINATES: similar to AA sequence:RefSeq:WP_012927294.1
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF017183.2
COORDINATES: protein motif:HMM:NF039534.1
COORDINATES: protein motif:HMM:NF016296.2
COORDINATES: protein motif:HMM:NF026255.2
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF018305.2
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018622795.1
COORDINATES: protein motif:HMM:NF033516.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
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_019986996.1
COORDINATES: protein motif:HMM:NF013188.2
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006885 - regulation of pH [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009282136.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020603366.1
COORDINATES: similar to AA sequence:RefSeq:WP_020598064.1
COORDINATES: similar to AA sequence:RefSeq:WP_018619822.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931456.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF022441.2
COORDINATES: protein motif:HMM:NF015531.2
COORDINATES: protein motif:HMM:NF014717.2
COORDINATES: protein motif:HMM:NF024116.2
COORDINATES: similar to AA sequence:RefSeq:WP_014678628.1
COORDINATES: similar to AA sequence:RefSeq:WP_018479520.1
sigma-54 dependent transcriptional regulator
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_020603785.1
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF014442.2
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF025052.2
COORDINATES: protein motif:HMM:TIGR00348.1
type I restriction endonuclease subunit R
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_019991204.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF021946.2
phage exclusion protein Lit family protein
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: similar to AA sequence:RefSeq:WP_020603043.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020602379.1
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020602378.1
COORDINATES: similar to AA sequence:RefSeq:WP_020603079.1
COORDINATES: similar to AA sequence:RefSeq:WP_018619748.1
COORDINATES: similar to AA sequence:RefSeq:WP_018619747.1
COORDINATES: similar to AA sequence:RefSeq:WP_020603360.1
COORDINATES: similar to AA sequence:RefSeq:WP_015332188.1
COORDINATES: similar to AA sequence:RefSeq:WP_012927339.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009280329.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014430.2
COORDINATES: protein motif:HMM:NF024972.2
zinc-dependent metalloprotease family protein
COORDINATES: protein motif:HMM:NF019205.2
COORDINATES: protein motif:HMM:TIGR01352.1
GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF039197.1
COORDINATES: similar to AA sequence:RefSeq:WP_018620965.1
COORDINATES: similar to AA sequence:RefSeq:WP_020596864.1
COORDINATES: similar to AA sequence:RefSeq:WP_012793325.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016640696.1
COORDINATES: protein motif:HMM:NF016648.2
COORDINATES: protein motif:HMM:TIGR04056.1
COORDINATES: similar to AA sequence:RefSeq:WP_019943518.1
RagB/SusD family nutrient uptake outer membrane protein
COORDINATES: protein motif:HMM:NF014850.2
glycoside hydrolase family 2 TIM barrel-domain containing protein
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_007804089.1
COORDINATES: similar to AA sequence:RefSeq:WP_010229987.1
COORDINATES: similar to AA sequence:RefSeq:WP_018618551.1
COORDINATES: protein motif:HMM:NF013698.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611505.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008239099.1
GO:0006812 - monoatomic cation transport [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: protein motif:HMM:NF024940.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: similar to AA sequence:RefSeq:WP_012930259.1
COORDINATES: similar to AA sequence:RefSeq:WP_020607384.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_009281175.1
COORDINATES: similar to AA sequence:RefSeq:WP_018345080.1
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012925830.1
COORDINATES: protein motif:HMM:NF013867.2
COORDINATES: protein motif:HMM:NF013502.2
COORDINATES: similar to AA sequence:RefSeq:WP_012792035.1
COORDINATES: protein motif:HMM:NF017853.2
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: similar to AA sequence:RefSeq:WP_009281931.1
COORDINATES: protein motif:HMM:TIGR02271.1
COORDINATES: similar to AA sequence:RefSeq:WP_018620321.1
COORDINATES: similar to AA sequence:RefSeq:WP_020606004.1
COORDINATES: similar to AA sequence:RefSeq:WP_020606005.1
COORDINATES: similar to AA sequence:RefSeq:WP_018618910.1
COORDINATES: similar to AA sequence:RefSeq:WP_020604689.1
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009284499.1
COORDINATES: similar to AA sequence:RefSeq:WP_012924757.1
COORDINATES: similar to AA sequence:RefSeq:WP_009283312.1
COORDINATES: similar to AA sequence:RefSeq:WP_018618916.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007139662.1
COORDINATES: similar to AA sequence:RefSeq:WP_010683323.1
COORDINATES: similar to AA sequence:RefSeq:WP_012928710.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931366.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931367.1
COORDINATES: similar to AA sequence:RefSeq:WP_020599845.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012931394.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_019990957.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_016193376.1
COORDINATES: protein motif:HMM:NF016807.2
COORDINATES: similar to AA sequence:RefSeq:WP_017455074.1
COORDINATES: protein motif:HMM:NF025495.2
GO:0004518 - nuclease activity [Evidence IEA]
dsDNA nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: similar to AA sequence:RefSeq:WP_011362333.1
COORDINATES: similar to AA sequence:RefSeq:WP_013997979.1
COORDINATES: similar to AA sequence:RefSeq:WP_015056753.1
COORDINATES: protein motif:HMM:NF021622.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015811783.1
COORDINATES: protein motif:HMM:NF018688.2
COORDINATES: similar to AA sequence:RefSeq:WP_012930513.1
COORDINATES: similar to AA sequence:RefSeq:WP_015329176.1
COORDINATES: similar to AA sequence:RefSeq:WP_012929211.1
COORDINATES: similar to AA sequence:RefSeq:WP_009284196.1
carboxypeptidase regulatory-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002732505.1
COORDINATES: similar to AA sequence:RefSeq:WP_020597342.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931286.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949548.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: protein motif:HMM:NF023227.2
COORDINATES: similar to AA sequence:RefSeq:WP_019990976.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931417.1
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017318392.1
COORDINATES: similar to AA sequence:RefSeq:WP_008468617.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_012927791.1
COORDINATES: similar to AA sequence:RefSeq:WP_012927792.1
COORDINATES: similar to AA sequence:RefSeq:WP_012927793.1
COORDINATES: protein motif:HMM:NF021524.2
COORDINATES: similar to AA sequence:RefSeq:WP_020607685.1
LytTR family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012925831.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_008512910.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931273.1
PDDEXK nuclease domain-containing protein