Rubrobacter tropicus strain SCSIO 52909 plasmid unnamed1, complete sequence.
Bacteria; Actinobacteria; Rubrobacteria; Rubrobacterales; Rubrobacteraceae; Rubrobacter.
Rubrobacter sp nov SCSIO 52090 isolated from a deep-sea sediment in the South China Sea
Submitted (11-OCT-2019) CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 Xingang West Road, Guangzhou, Guangdong 510301, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP045120.1.\nBacteria and source DNA available from XP TIAN.\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 Method :: Celera Assembler v. 8.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 250.0x\nSequencing Technology :: Illumina HiSeq 4000\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/24/2022 01:23:16\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\nGenes (total) :: 4,643\nCDSs (total) :: 4,588\nGenes (coding) :: 4,540\nCDSs (with protein) :: 4,540\nGenes (RNA) :: 55\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 48\nCDSs (without protein) :: 48\nPseudo Genes (ambiguous residues) :: 0 of 48\nPseudo Genes (frameshifted) :: 10 of 48\nPseudo Genes (incomplete) :: 37 of 48\nPseudo Genes (internal stop) :: 4 of 48\nPseudo Genes (multiple problems) :: 3 of 48\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF018028.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024367.2
COORDINATES: protein motif:HMM:NF025186.2
COORDINATES: similar to AA sequence:RefSeq:WP_013449717.1
COORDINATES: protein motif:HMM:TIGR00614.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011563044.1
COORDINATES: similar to AA sequence:RefSeq:WP_017569189.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_010496434.1
COORDINATES: similar to AA sequence:RefSeq:WP_017597509.1
COORDINATES: similar to AA sequence:RefSeq:WP_014510137.1
metal-dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004436790.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF016149.2
COORDINATES: similar to AA sequence:RefSeq:WP_011563580.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563579.1
COORDINATES: protein motif:HMM:NF016119.2
COORDINATES: protein motif:HMM:TIGR01076.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565361.1
COORDINATES: protein motif:HMM:NF016202.2
peptidoglycan binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012872993.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563650.1
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013080.2
COORDINATES: protein motif:HMM:NF017722.2
COORDINATES: protein motif:HMM:NF014703.2
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0050380 - undecaprenyl-diphosphatase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]; GO:0046677 - response to antibiotic [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013524285.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563584.1
COORDINATES: similar to AA sequence:RefSeq:WP_013130707.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011563583.1
cation diffusion facilitator family transporter
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: similar to AA sequence:RefSeq:WP_013496408.1
COORDINATES: similar to AA sequence:RefSeq:WP_014811315.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_015231623.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435802.1
COORDINATES: protein motif:HMM:NF020123.2
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014375670.1
COORDINATES: protein motif:HMM:NF013915.2
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_011565721.1
COORDINATES: protein motif:HMM:NF023650.2
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: similar to AA sequence:RefSeq:WP_018863756.1
COORDINATES: similar to AA sequence:RefSeq:WP_012873326.1
COORDINATES: similar to AA sequence:RefSeq:WP_012302948.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563129.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010650470.1
GO:0005507 - copper ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011563127.1
COORDINATES: protein motif:HMM:NF012566.2
heavy metal-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008169443.1
COORDINATES: similar to AA sequence:RefSeq:WP_008930118.1
COORDINATES: similar to AA sequence:RefSeq:WP_008930119.1
GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
GO:0042773 - ATP synthesis coupled electron transport [Evidence IEA]
NADH-quinone oxidoreductase subunit NuoK
COORDINATES: similar to AA sequence:RefSeq:WP_008169449.1
proton-conducting transporter membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011563121.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563120.1
COORDINATES: protein motif:HMM:NF012790.2
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018404633.1
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: protein motif:HMM:NF014043.2
COORDINATES: similar to AA sequence:RefSeq:WP_004037656.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF025605.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF013491.2
GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007557659.1
COORDINATES: protein motif:HMM:NF015715.2
COORDINATES: similar to AA sequence:RefSeq:WP_011159102.1
COORDINATES: protein motif:HMM:NF024248.2
COORDINATES: similar to AA sequence:RefSeq:WP_012871853.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565798.1
COORDINATES: similar to AA sequence:RefSeq:WP_014813074.1
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_007910121.1
GO:0015267 - channel activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF033527.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: similar to AA sequence:RefSeq:WP_010149454.1
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF016184.2
GO:0016787 - hydrolase activity [Evidence IEA]
sulfur transferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012374290.1
COORDINATES: similar to AA sequence:RefSeq:WP_012692189.1
COORDINATES: similar to AA sequence:RefSeq:WP_006927944.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006431727.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006528085.1
GO:0004671 - protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity [Evidence IEA]
protein-S-isoprenylcysteine O-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_002856921.1
phenylacetate--CoA ligase family protein
COORDINATES: protein motif:HMM:TIGR00077.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015328586.1
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: protein motif:HMM:NF015155.2
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF012493.2
COORDINATES: protein motif:HMM:TIGR00498.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006282 - regulation of DNA repair [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00594.1
COORDINATES: protein motif:HMM:NF015513.2
COORDINATES: protein motif:HMM:NF025744.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF012298.2
Stk1 family PASTA domain-containing Ser/Thr kinase
COORDINATES: similar to AA sequence:RefSeq:WP_005816793.1
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: similar to AA sequence:RefSeq:WP_014600193.1
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF040105.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012403.2
COORDINATES: protein motif:HMM:NF028103.2
DNA-primase RepB domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019653749.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_011565794.1
vitamin B12-dependent ribonucleotide reductase
COORDINATES: similar to AA sequence:RefSeq:WP_011565560.1
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]
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: protein motif:HMM:NF015022.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF014044.2