Simplicispira suum strain SC1-8 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Simplicispira.
Submitted (09-MAR-2018) 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\nCP027670.1.\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 Date :: FEB-2018\nAssembly Method :: RS HGAP Assembly v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 159.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 22:45:25\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) :: 3,904\nCDSs (total) :: 3,840\nGenes (coding) :: 3,747\nCDSs (with protein) :: 3,747\nGenes (RNA) :: 64\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 3\nPseudo Genes (total) :: 93\nCDSs (without protein) :: 93\nPseudo Genes (ambiguous residues) :: 0 of 93\nPseudo Genes (frameshifted) :: 50 of 93\nPseudo Genes (incomplete) :: 47 of 93\nPseudo Genes (internal stop) :: 7 of 93\nPseudo Genes (multiple problems) :: 9 of 93\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_013516267.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013516269.1
COORDINATES: similar to AA sequence:RefSeq:WP_005792643.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049914.1
COORDINATES: similar to AA sequence:RefSeq:WP_006746770.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008449156.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516294.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516288.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516302.1
COORDINATES: protein motif:HMM:NF013506.2
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012435588.1
COORDINATES: similar to AA sequence:RefSeq:WP_000414383.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:WP_013722692.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001277466.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005229645.1
COORDINATES: similar to AA sequence:RefSeq:WP_000904941.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221021.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [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:YP_005221000.1
IS6-like element IS26 family transposase
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_001256773.1
chloramphenicol efflux MFS transporter CmlA1
COORDINATES: similar to AA sequence:RefSeq:WP_001749984.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
AadA family aminoglycoside 3''-O-nucleotidyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1
quaternary ammonium compound efflux SMR transporter QacE delta 1
COORDINATES: similar to AA sequence:RefSeq:WP_000259031.1
sulfonamide-resistant dihydropteroate synthase Sul1
COORDINATES: similar to AA sequence:RefSeq:WP_004194535.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229646.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
IS6-like element IS6100 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011342941.1
COORDINATES: similar to AA sequence:RefSeq:WP_011342942.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_011514928.1
GO:0020037 - heme binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_008265574.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_020230035.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013516331.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015913602.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516329.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516328.1
COORDINATES: similar to AA sequence:RefSeq:WP_017159824.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013516326.1
COORDINATES: similar to AA sequence:RefSeq:WP_020424931.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516324.1
COORDINATES: similar to AA sequence:RefSeq:WP_018079567.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516337.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516338.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516339.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516226.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013516227.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516228.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516230.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516231.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516232.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516233.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_013516234.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516235.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516236.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516237.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576702.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_013516241.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013516242.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_013516243.1
COORDINATES: protein motif:HMM:TIGR02747.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_019576697.1
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_013516246.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516247.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516248.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516249.1
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_013516250.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516251.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516252.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516253.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516254.1
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013516255.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516256.1
fibronectin type III domain-containing protein
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_015472820.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005927424.1
COORDINATES: similar to AA sequence:RefSeq:WP_005348800.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805797.1
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF024486.2
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:TIGR00616.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: similar to AA sequence:RefSeq:WP_008343193.1
COORDINATES: similar to AA sequence:RefSeq:WP_013801349.1
COORDINATES: protein motif:HMM:NF024601.2
COORDINATES: similar to AA sequence:RefSeq:WP_011831703.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516262.1