Sphingomonas daechungensis strain KACC 18115 plasmid p_unnamed1.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Genome sequence of Sphingomonas daechungensis KACC 18115T
Submitted (26-AUG-2020) Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP060781.1.\nBacteria and source DNA available from KACC 18115.\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 :: HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 230.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/09/2022 05:09:49\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) :: 3,507\nCDSs (total) :: 3,454\nGenes (coding) :: 2,789\nCDSs (with protein) :: 2,789\nGenes (RNA) :: 53\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 665\nCDSs (without protein) :: 665\nPseudo Genes (ambiguous residues) :: 0 of 665\nPseudo Genes (frameshifted) :: 590 of 665\nPseudo Genes (incomplete) :: 115 of 665\nPseudo Genes (internal stop) :: 4 of 665\nPseudo Genes (multiple problems) :: 44 of 665\n##Genome-Annotation-Data-END##
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024896.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF028277.2
TcfC E-set like domain-containing protein
COORDINATES: protein motif:HMM:NF027306.2
CS1-pili formation C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012565.2
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0071555 - cell wall organization [Evidence IEA]
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF024934.2
Crp/Fnr family transcriptional regulator
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: protein motif:HMM:TIGR02595.1
PEPxxWA-CTERM sorting domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019052009.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049184.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054413.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008193953.1
COORDINATES: protein motif:HMM:NF012257.2
COORDINATES: similar to AA sequence:RefSeq:WP_019465632.1
carbon-nitrogen hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010185186.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832912.1
COORDINATES: similar to AA sequence:RefSeq:WP_015159451.1
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019450598.1
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_020177164.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_008994732.1
COORDINATES: protein motif:HMM:NF013254.2
phosphoribosylglycinamide synthetase C domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017503452.1
iron-containing redox enzyme family protein
COORDINATES: protein motif:HMM:NF017026.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017364605.1
GO:0003700 - DNA-binding transcription factor 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.
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_013837076.1
ArsI/CadI family heavy metal resistance metalloenzyme
COORDINATES: similar to AA sequence:RefSeq:WP_018182504.1
COORDINATES: similar to AA sequence:RefSeq:WP_008144259.1
COORDINATES: similar to AA sequence:RefSeq:WP_007663553.1
histidine kinase dimerization/phosphoacceptor domain -containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005663033.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007511091.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186583.1
COORDINATES: similar to AA sequence:RefSeq:WP_020184244.1
COORDINATES: similar to AA sequence:RefSeq:WP_007416386.1
COORDINATES: similar to AA sequence:RefSeq:WP_020070968.1
COORDINATES: similar to AA sequence:RefSeq:WP_020092815.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009570975.1
COORDINATES: similar to AA sequence:RefSeq:WP_006833374.1
GO:0003743 - translation initiation factor activity [Evidence IEA]
GO:0006413 - translational initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501134.1
COORDINATES: protein motif:HMM:NF025539.2
COORDINATES: similar to AA sequence:RefSeq:WP_005628339.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_013714246.1
(deoxy)nucleoside triphosphate pyrophosphohydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_009107961.1
HNH endonuclease signature motif containing protein
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF015898.2
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: protein motif:HMM:NF019335.2
TonB-dependent receptor plug domain-containing protein
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF015513.2
COORDINATES: protein motif:HMM:NF018305.2
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF012301.2
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: protein motif:HMM:NF016296.2
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024592.2
COORDINATES: similar to AA sequence:RefSeq:WP_009211255.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017979281.1
COORDINATES: similar to AA sequence:RefSeq:WP_000842106.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_012252461.1
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_010127568.1
COORDINATES: similar to AA sequence:RefSeq:WP_011003357.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009209325.1
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: protein motif:HMM:NF013866.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015458915.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004494 - methylmalonyl-CoA mutase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018684.2
COORDINATES: similar to AA sequence:RefSeq:WP_019369976.1
acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
COORDINATES: protein motif:HMM:NF021982.2
COORDINATES: similar to AA sequence:RefSeq:WP_007685838.1
COORDINATES: similar to AA sequence:RefSeq:WP_017099480.1
COORDINATES: similar to AA sequence:RefSeq:WP_010214961.1
COORDINATES: similar to AA sequence:RefSeq:WP_013566987.1
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_019341434.1
GO:0008767 - UDP-galactopyranose mutase activity [Evidence IEA]
GO:0009273 - peptidoglycan-based cell wall biogenesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF012457.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF016228.2
COORDINATES: similar to AA sequence:RefSeq:WP_013834450.1
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity [Evidence IEA]
GO:0006094 - gluconeogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013041339.1
COORDINATES: protein motif:HMM:NF013300.2
GO:0004560 - alpha-L-fucosidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019896.2
D-Ala-D-Ala carboxypeptidase family metallohydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_007165259.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011951373.1
trimeric intracellular cation channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010406628.1
GO:0016746 - acyltransferase activity [Evidence IEA]
GO:0042619 - poly-hydroxybutyrate biosynthetic process [Evidence IEA]
class I poly(R)-hydroxyalkanoic acid synthase
COORDINATES: similar to AA sequence:RefSeq:WP_017666701.1
COORDINATES: protein motif:HMM:TIGR00688.1
GO:0005887 - integral component of plasma membrane [Evidence IEA]
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF027558.2
COORDINATES: similar to AA sequence:RefSeq:WP_017978996.1
COORDINATES: similar to AA sequence:RefSeq:WP_017671239.1
COORDINATES: similar to AA sequence:RefSeq:WP_010407355.1
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020486444.1
COORDINATES: protein motif:HMM:NF012832.2
COORDINATES: protein motif:HMM:NF020918.2
COORDINATES: similar to AA sequence:RefSeq:WP_008602869.1
COORDINATES: protein motif:HMM:NF012497.2
COORDINATES: similar to AA sequence:RefSeq:WP_006952370.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
frameshifted; 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.