Sphingomonas aliaeris strain DH-S5 plasmid punnamed1, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere
Submitted (01-SEP-2020) Institute for Food Microbiology and Hygiene, University of Bonn, Endenicher Allee 19 B, Bonn 53115, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP061036.1.\nBacteria and source DNA available from Food microbiology and\nhygiene, University of Bonn, Endenicher Allee 19B, 53115 Bonn.\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 Date :: MAR-2020\nAssembly Method :: flye assembly tool v. 2.7b\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 56.0x\nSequencing Technology :: Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/25/2022 04:38:31\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) :: 4,133\nCDSs (total) :: 4,076\nGenes (coding) :: 3,792\nCDSs (with protein) :: 3,792\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 284\nCDSs (without protein) :: 284\nPseudo Genes (ambiguous residues) :: 0 of 284\nPseudo Genes (frameshifted) :: 234 of 284\nPseudo Genes (incomplete) :: 57 of 284\nPseudo Genes (internal stop) :: 12 of 284\nPseudo Genes (multiple problems) :: 17 of 284\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_019054292.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010409256.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: similar to AA sequence:RefSeq:WP_007406613.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406323.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409251.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406314.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054285.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_006953574.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460511.1
COORDINATES: protein motif:HMM:TIGR02742.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007406329.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406347.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406358.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010161711.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008603814.1
COORDINATES: similar to AA sequence:RefSeq:WP_019370813.1
COORDINATES: similar to AA sequence:RefSeq:WP_012382806.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406362.1
COORDINATES: similar to AA sequence:RefSeq:WP_008997207.1
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010409149.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949446.1
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: similar to AA sequence:RefSeq:WP_010405773.1
COORDINATES: similar to AA sequence:RefSeq:WP_016509811.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016509327.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF033580.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010409132.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510756.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510716.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409121.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510753.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251239.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339725.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510947.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250443.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250446.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250447.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409093.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409090.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510253.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409084.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183274.1
COORDINATES: similar to AA sequence:RefSeq:WP_003056809.1
GO:0008168 - methyltransferase activity [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_006953725.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409079.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832690.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250438.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510267.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250454.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408929.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510268.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408925.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124620.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829632.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408914.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510938.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405810.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:TIGR00180.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950527.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408880.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010408871.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219642.1
COORDINATES: similar to AA sequence:RefSeq:WP_010189052.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339761.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010339514.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830456.1
COORDINATES: protein motif:HMM:NF024853.2
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008830454.1
COORDINATES: protein motif:HMM:NF020123.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251198.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018251197.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830450.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008830449.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830448.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994503.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994502.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]; GO:0008379 - thioredoxin peroxidase activity [Evidence IEA]
GO:0098869 - cellular oxidant detoxification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018265946.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_008830444.1
COORDINATES: similar to AA sequence:RefSeq:WP_012048460.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368253.1
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_010217637.1
COORDINATES: similar to AA sequence:RefSeq:WP_015318511.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980826.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_011542808.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007404395.1
sulfurtransferase/chromate resistance protein
COORDINATES: similar to AA sequence:RefSeq:WP_019370515.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF037472.2
COORDINATES: similar to AA sequence:RefSeq:WP_008603797.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165237.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_004210818.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007406848.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010501318.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251375.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
CDF family Co(II)/Ni(II) efflux transporter DmeF
COORDINATES: similar to AA sequence:RefSeq:WP_010165246.1
COORDINATES: similar to AA sequence:RefSeq:WP_017505540.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980773.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368240.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501296.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183605.1
COORDINATES: similar to AA sequence:RefSeq:WP_015314946.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368245.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368246.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_019368247.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368248.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165215.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368250.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_019368251.1
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_007407020.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010219218.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165232.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368266.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010127314.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950386.1
COORDINATES: similar to AA sequence:RefSeq:WP_010123226.1
COORDINATES: similar to AA sequence:RefSeq:WP_007705697.1
COORDINATES: similar to AA sequence:RefSeq:WP_004210791.1
COORDINATES: protein motif:HMM:NF022072.2
COORDINATES: similar to AA sequence:RefSeq:WP_010405582.1
COORDINATES: similar to AA sequence:RefSeq:WP_003046522.1
COORDINATES: similar to AA sequence:RefSeq:WP_008874686.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368193.1
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_018251250.1
COORDINATES: similar to AA sequence:RefSeq:WP_013384096.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015371.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212886.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005215 - transporter activity [Evidence IEA]
frameshifted; 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_010124851.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092652.1
COORDINATES: similar to AA sequence:RefSeq:WP_005666236.1
GO:0005515 - protein binding [Evidence IEA]
PAS domain-containing hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007406249.1
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018264113.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019998550.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012850369.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510730.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409231.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014074677.1
COORDINATES: protein motif:HMM:NF025714.2
COORDINATES: protein motif:HMM:NF025013.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251281.1
COORDINATES: similar to AA sequence:RefSeq:WP_007404100.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018251279.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018251278.1
COORDINATES: protein motif:HMM:NF015048.2
COORDINATES: similar to AA sequence:RefSeq:WP_010339518.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339517.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010339516.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251272.1
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_018251271.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251270.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251269.1
COORDINATES: protein motif:HMM:NF019174.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251268.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251266.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251265.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251263.1
COORDINATES: protein motif:HMM:NF020859.2
Mu transposase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF020606.2
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_006727821.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014076289.1
type IV toxin-antitoxin system AbiEi family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010218631.1
COORDINATES: protein motif:HMM:NF012376.2
COORDINATES: protein motif:HMM:NF014516.2
COORDINATES: similar to AA sequence:RefSeq:WP_012116660.1
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_004672925.1
COORDINATES: similar to AA sequence:RefSeq:WP_019905962.1
COORDINATES: similar to AA sequence:RefSeq:WP_018291663.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008832026.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460523.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_010409259.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_007406304.1
type-F conjugative transfer system secretin TraK