LOCUS       CP027424                2473 bp    DNA     circular BCT 27-SEP-2019
DEFINITION  Staphylococcus cohnii strain FDAARGOS_334 plasmid unnamed5, complete
            sequence.
ACCESSION   CP027424
VERSION     CP027424.1
DBLINK      BioProject: PRJNA231221
            BioSample: SAMN06173347
KEYWORDS    .
SOURCE      Staphylococcus cohnii
  ORGANISM  Staphylococcus cohnii
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2473)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Sengamalay,N.,
            Ott,S., Godinez,A., Nagaraj,S., Vavikolanu,K., Vyas,G., Nadendla,S.,
            Aluvathingal,J., Geyer,C., Nandy,P., Hobson,J. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2473)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Sengamalay,N.,
            Ott,S., Godinez,A., Nagaraj,S., Vavikolanu,K., Vyas,G., Nadendla,S.,
            Aluvathingal,J., Geyer,C., Nandy,P., Hobson,J. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-MAR-2018) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 2.3.0, HGAP v. 3.0
            Genome Coverage                   :: 715.575x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/02/2018 12:14:18
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            Annotation Method :: Best-placed reference protein set; GeneMarkS+
            Annotation Software revision      :: 4.4
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 2,584
            CDS (total)                       :: 2,503
            Genes (coding)                    :: 2,433
            CDS (coding)                      :: 2,433
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 70
            Pseudo Genes (ambiguous residues) :: 0 of 70
            Pseudo Genes (frameshifted)       :: 44 of 70
            Pseudo Genes (incomplete)         :: 18 of 70
            Pseudo Genes (internal stop)      :: 19 of 70
            Pseudo Genes (multiple problems)  :: 11 of 70
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..2473
                     /organism="Staphylococcus cohnii"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_334"
                     /isolation_source="Peripheral blood"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_334"
                     /db_xref="taxon:29382"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: DC"
                     /collection_date="22-Feb-2015"
                     /collected_by="Children's National Hospital"
     gene            complement(538..1014)
                     /locus_tag="CEQ12_12915"
     CDS             complement(538..1014)
                     /locus_tag="CEQ12_12915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication and maintenance protein"
                     /protein_id="AVL78668.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication and maintenance protein"
     gene            complement(1462..2196)
                     /locus_tag="CEQ12_12920"
     CDS             complement(1462..2196)
                     /locus_tag="CEQ12_12920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011282421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /protein_id="AVL78669.1"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFT
                     LELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPY
                     NISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYF
                     HPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGID
                     DLNNISFEQFLSLFNSYKLFNK"
                     /name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
     ARG             complement(1466..2196)
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1463..2196)
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          complement(529..1014)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttcttaaa ggttttatac ttttggtcgt agagcacacg gtttaacgac ttaattacga
       61 agtaaataag tctagtgtgt tagactttaa tgttttttta aggcattagt gcatttaagc
      121 gtcagagcat ggctttatgc cgagaaaact attggttgga atggcgtgtg tgttagccaa
      181 agctttggcg agttggttgg gggtttcatg ggattaatcc catgaaagta ccaactcaac
      241 aacacactaa cgcctgttgg ttccaaccaa taggaaattg gaataagcaa ttagtataat
      301 gagagtataa tgttggtata acgttagtat aatgatgctt tttttcatta tattttttat
      361 gtactttaaa cctgcacgct tatgtgaatt agaaaaagct taatcgcatt tcatagattg
      421 acctcccaat aactacgtgg tgttattggg aggtcaatct atttcatttg cgttaagctt
      481 ttgatctaca ttaagcgtgc aggttttttg tctatttgta gacgatttta tgttatacta
      541 gtccttgaaa gaataataat cagataatgc attttcttgt ttttcatttg cctcttgctc
      601 aaagttccca aattcgagta agaggtattt ttgtttttgg tcgtcgcctc tcattagtag
      661 ttcagggttt aacattaata ctccagtttt tctttttata atatttcctt cttctaagat
      721 tttaagtgtt gttattactg tttgtagact tgttcctgta gcttttgcta tttctcttgt
      781 tgtagctatc attgtattgt tacttaagtg gacattatct aggatatagt taacgatttt
      841 aagttttttt ccgccaatca tatctaacat acttattaat tgcactatat atgcctttac
      901 gaagttacca gacgtttgtt tacggtataa cttgtctacc tctatgactt ctccactttc
      961 ttcgtctatg agcctctgag agcctttata gactgttcca tatctttctt tcatcttttt
     1021 ctcactcctt attttaaact attctaacta tatcataact gttctaaaaa aaaaagaaca
     1081 tttgttaaaa gaaattagaa caaaatgagt gaaaaattag aacaaacaaa ttccttataa
     1141 accttatcat ctcaacctat attaagattt tacctagttg aatcttcttt tctatataaa
     1201 gcgtcggagc atatcagggg gttatctaac gtaaatgcta cccttcggct cgctttcgct
     1261 cggcattgac gtcagatact gcaccccctg aacccccatg ctccaacagc aaaaaggaaa
     1321 ctttttgctg cttttccgac gcttattcgc ttcgctcata tttatataga aaagaagtga
     1381 atgcgcaaaa gacataatcg attcacaaaa aataggtaca cgaaaaacaa gttaagggat
     1441 gcagtttatg catcccttaa cttacttatt aaataattta tagctattga aaagagataa
     1501 gaattgttca aagctaatat tgtttaaatc gtcaattcct gcatgtttta aggaattgtt
     1561 aaattgattt tttgtaaata ttttcttgta ttctttgtta acccatttca taacgaaata
     1621 attatacttc tgtttatctt tgtgtgatat tcttgatttt tttctattta atctgataag
     1681 tgagctattc actttaggtt taggatgaaa atattctctt ggaaccatac ttaatataga
     1741 aatatcaact tctgccatta aaaataatgc caatgagcgt tttgtattta ataatctttt
     1801 agcaaacccg tattccacga ttaaataaat ctcatcagct atactatcaa aaacaatttt
     1861 gcgtattata tccgtactta tgttataagg tatattacca aatattttat aggattggtt
     1921 tttaggaaat ttaaactgca atatatcctt gtttaaaact tggaaattat cgtgatcaac
     1981 aagtttattt tctgtagttt tgcataattt atggtctatt tcaatggcag ttacgaaatt
     2041 acacctctgt actaattcaa gggtaaaatg cccttttcct gagccgattt caaagatatt
     2101 atcatgttca tttaatctta tatttgtcat tattttatct atattatgtt ttgaagtaat
     2161 aaagttttga ctgtgtttta tatttttctc gttcattata accctcttta atttggttat
     2221 aatgaatttt gcttattaac gattcattat aaccacttat tttttgtttg gttgataatg
     2281 aactgtgctg attacaaaaa tactaaaaat gcccatattt tttcctcctt ataaaattag
     2341 tataattata gcacgagctc tgataaatat gaacatgatg agtgatcgtt aaatttatac
     2401 tgcaatctga tgcgattatt gaataaaaga tatgagagat ttatctagtt tcttttttta
     2461 caagaaaaaa gaa
//
