Sphingomonas insulae strain KCTC 12872 plasmid unnamed3, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Genome sequence of Sphingomonas insulae KCTC 12872
Submitted (06-JAN-2020) Agriculture & Life Science, Kyungpook National University, Daehak-ro 80, Daegu 41566, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP048421.1.\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 Date :: 06-JAN-2020\nAssembly Method :: HGAP v. 4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 276.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 02:15:08\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) :: 3,611\nCDSs (total) :: 3,546\nGenes (coding) :: 3,472\nCDSs (with protein) :: 3,472\nGenes (RNA) :: 65\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 3\nPseudo Genes (total) :: 74\nCDSs (without protein) :: 74\nPseudo Genes (ambiguous residues) :: 0 of 74\nPseudo Genes (frameshifted) :: 57 of 74\nPseudo Genes (incomplete) :: 18 of 74\nPseudo Genes (internal stop) :: 3 of 74\nPseudo Genes (multiple problems) :: 4 of 74\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
GO:0009060 - aerobic respiration [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
cbb3-type cytochrome c oxidase subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_017978073.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010239998.1
COORDINATES: similar to AA sequence:RefSeq:WP_010402679.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008828908.1
COORDINATES: similar to AA sequence:RefSeq:WP_019516244.1
COORDINATES: similar to AA sequence:RefSeq:WP_010184460.1
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_005670224.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219193.1
sensor domain-containing diguanylate cyclase
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_015951647.1
COORDINATES: similar to AA sequence:RefSeq:WP_010184975.1
COORDINATES: similar to AA sequence:RefSeq:WP_019515359.1
COORDINATES: similar to AA sequence:RefSeq:WP_013378022.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008828045.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076611470.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011906605.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF022400.2
COORDINATES: protein motif:HMM:NF021378.2
COORDINATES: similar to AA sequence:RefSeq:WP_020818220.1
COORDINATES: similar to AA sequence:RefSeq:WP_007710491.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003535419.1
COORDINATES: similar to AA sequence:RefSeq:WP_019184203.1
COORDINATES: similar to AA sequence:RefSeq:WP_003519273.1
COORDINATES: similar to AA sequence:RefSeq:WP_007666328.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019466717.1
COORDINATES: similar to AA sequence:RefSeq:WP_019370527.1
COORDINATES: similar to AA sequence:RefSeq:WP_013040277.1
COORDINATES: similar to AA sequence:RefSeq:WP_007092231.1
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010216103.1
COORDINATES: similar to AA sequence:RefSeq:WP_020486340.1
COORDINATES: similar to AA sequence:RefSeq:WP_012322182.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017979276.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406924.1
COORDINATES: protein motif:HMM:TIGR01782.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014005185.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013480866.1
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010546066.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015535 - fucose:proton symporter activity [Evidence IEA]
GO:0015756 - fucose transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018430407.1
COORDINATES: similar to AA sequence:RefSeq:WP_007830385.1
COORDINATES: similar to AA sequence:RefSeq:WP_004208375.1
COORDINATES: similar to AA sequence:RefSeq:WP_006275216.1
COORDINATES: protein motif:HMM:NF013276.2
GO:0030599 - pectinesterase activity [Evidence IEA]
GO:0042545 - cell wall modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013053821.1
COORDINATES: similar to AA sequence:RefSeq:WP_010163277.1
DNA starvation/stationary phase protection protein
COORDINATES: similar to AA sequence:RefSeq:WP_010216094.1
COORDINATES: similar to AA sequence:RefSeq:WP_010163035.1
COORDINATES: similar to AA sequence:RefSeq:WP_008575709.1
COORDINATES: similar to AA sequence:RefSeq:WP_013395811.1
COORDINATES: similar to AA sequence:RefSeq:WP_007705684.1
COORDINATES: similar to AA sequence:RefSeq:WP_013479902.1
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF014566.2
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_003041004.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832546.1
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:NF012437.2
GO:0009190 - cyclic nucleotide biosynthetic process [Evidence IEA]; GO:0035556 - intracellular signal transduction [Evidence IEA]
adenylate/guanylate cyclase domain-containing protein
COORDINATES: protein motif:HMM:NF040152.1
COORDINATES: protein motif:HMM:NF023178.2
COORDINATES: similar to AA sequence:RefSeq:WP_017299803.1
COORDINATES: similar to AA sequence:RefSeq:WP_003564941.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014421489.1
COORDINATES: similar to AA sequence:RefSeq:WP_006718411.1
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001546962.1
COORDINATES: similar to AA sequence:RefSeq:WP_010511758.1
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251297.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251298.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188921.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980866.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017500352.1
COORDINATES: similar to AA sequence:RefSeq:WP_006964375.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980864.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251301.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251303.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219630.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_017980859.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_010188876.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980732.1
COORDINATES: similar to AA sequence:RefSeq:WP_020486659.1
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980856.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219623.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_010219622.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980727.1
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_017980852.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007790102.1
GO:0009055 - electron transfer activity [Evidence IEA]
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013947192.1
COORDINATES: similar to AA sequence:RefSeq:WP_014189156.1
putative sulfate exporter family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_010504628.1
COORDINATES: similar to AA sequence:RefSeq:WP_012333565.1
COORDINATES: similar to AA sequence:RefSeq:WP_020179900.1
COORDINATES: similar to AA sequence:RefSeq:WP_017500308.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017980904.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188850.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054090.1
COORDINATES: similar to AA sequence:RefSeq:WP_010186664.1
alpha-ketoglutarate-dependent dioxygenase AlkB
COORDINATES: similar to AA sequence:RefSeq:WP_019831671.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018251308.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188528.1
COORDINATES: similar to AA sequence:RefSeq:WP_010161708.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251294.1
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_010339751.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188795.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251311.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251312.1
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_013849896.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165449.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013849894.1
COORDINATES: protein motif:HMM:NF016836.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251150.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165180.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165182.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165183.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165184.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165185.1
GO:0003824 - catalytic activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188938.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010165188.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188936.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831578.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165196.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980767.1
COORDINATES: protein motif:HMM:NF017206.2
COORDINATES: protein motif:HMM:NF028169.2
COORDINATES: similar to AA sequence:RefSeq:WP_011503487.1
GO:0005515 - protein binding [Evidence IEA]
hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007537480.1
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: protein motif:HMM:NF013736.2
COORDINATES: similar to AA sequence:RefSeq:WP_010165265.1
COORDINATES: similar to AA sequence:RefSeq:WP_017967257.1
COORDINATES: similar to AA sequence:RefSeq:WP_009027389.1
COORDINATES: similar to AA sequence:RefSeq:WP_007014616.1
COORDINATES: similar to AA sequence:RefSeq:WP_010337160.1
COORDINATES: similar to AA sequence:RefSeq:WP_011445771.1
GO:0030416 - methylamine metabolic process [Evidence IEA]
MauE/DoxX family redox-associated membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_017916216.1
COORDINATES: similar to AA sequence:RefSeq:WP_012287066.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503872.1
COORDINATES: similar to AA sequence:RefSeq:WP_015235998.1
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054131.1
COORDINATES: similar to AA sequence:RefSeq:WP_010185246.1
COORDINATES: similar to AA sequence:RefSeq:WP_008135207.1
COORDINATES: protein motif:HMM:NF015338.2
endonuclease/exonuclease/phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019516402.1
GO:0016020 - membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0048038 - quinone binding [Evidence IEA]
membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
COORDINATES: similar to AA sequence:RefSeq:WP_010238185.1
COORDINATES: similar to AA sequence:RefSeq:WP_008599840.1
COORDINATES: similar to AA sequence:RefSeq:WP_007164038.1
COORDINATES: protein motif:HMM:NF022039.2
COORDINATES: similar to AA sequence:RefSeq:WP_019517612.1
COORDINATES: similar to AA sequence:RefSeq:WP_019517696.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019368650.1
COORDINATES: protein motif:HMM:NF015587.2
YihY/virulence factor BrkB family protein
COORDINATES: protein motif:HMM:NF013740.2
COORDINATES: protein motif:HMM:NF015679.2
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009823601.1
cytochrome C oxidase subunit IV family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017978075.1