LOCUS       NZ_CP070119             3319 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1298 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP070119
VERSION     NZ_CP070119.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357440
            Assembly: GCF_016904455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3319)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. 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  JOURNAL   Unpublished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 3319)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-FEB-2021) Institute for Genome Sciences, University of
            Maryland School of Medicine, BioPark II, 801 W. Baltimore St., Suite
            619, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 8.0.0, HGAP v. 4
            Genome Coverage                   :: 963.3x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:37:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,299
            CDSs (total)                      :: 5,180
            Genes (coding)                    :: 4,969
            CDSs (with protein)               :: 4,969
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 78 of 211
            Pseudo Genes (incomplete)         :: 128 of 211
            Pseudo Genes (internal stop)      :: 48 of 211
            Pseudo Genes (multiple problems)  :: 40 of 211
            Pseudo Genes (short protein)      :: 4 of 211
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070119.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3319
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1298"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1298"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(360..554)
                     /locus_tag="I6K28_RS26135"
                     /old_locus_tag="I6K28_26075"
     CDS             complement(360..554)
                     /locus_tag="I6K28_RS26135"
                     /old_locus_tag="I6K28_26075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041620.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            839..1162
                     /gene="mobA"
                     /locus_tag="I6K28_RS26140"
                     /old_locus_tag="I6K28_26080"
     CDS             839..1162
                     /gene="mobA"
                     /locus_tag="I6K28_RS26140"
                     /old_locus_tag="I6K28_26080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1397..1777)
                     /gene="lsoB"
                     /locus_tag="I6K28_RS26145"
                     /old_locus_tag="I6K28_26085"
     CDS             complement(1397..1777)
                     /gene="lsoB"
                     /locus_tag="I6K28_RS26145"
                     /old_locus_tag="I6K28_26085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /protein_id="WP_000710826.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(1774..2814)
                     /gene="lsoA"
                     /locus_tag="I6K28_RS26150"
                     /old_locus_tag="I6K28_26090"
     CDS             complement(1774..2814)
                     /gene="lsoA"
                     /locus_tag="I6K28_RS26150"
                     /old_locus_tag="I6K28_26090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /protein_id="WP_047938481.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HRETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            complement(3079..3192)
                     /locus_tag="I6K28_RS26635"
     CDS             complement(3079..3192)
                     /locus_tag="I6K28_RS26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001459398.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="hypothetical protein"
     Typing          590..830
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.12e-123"
     Typing          complement(2..172)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="100.0"
                     /evalue="1.4699999999999995e-67"
     Typing          complement(3121..3319)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.5"
                     /coverage="99.0"
                     /evalue="5.26e-98"
     Typing          840..1159
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.76e-62"
ORIGIN
        1 ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg
       61 tttcgccacc tctggcttga gcgtcgattt ttgtgatgct cgtcaggggg gcggagccta
      121 tggaaaaacg cctgcagcgt tggcttcttc cggtgctttg ctttttgctc acatgttctt
      181 tccggcttta tcccctgatt ctgtggataa ccgtattacc gcttttgagt gagctgacac
      241 cgctcgccgc agtcgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg
      301 ccttatgtga cattttctcc ttacgctctg ttgtgccgtt cggcatcctg tcctgagagt
      361 tatctctctg tgctattttc tacttcaaag cgtgtctgga tgctgttctg gagttcttct
      421 gcgagttcgt gcagcttctc acacatggca gcctgttcgt cagcatcgag tgcgtccagc
      481 ttttcgagca gcgtcaggct ctggcttttt atgaatcctg ccatgttgag tacagcttgc
      541 tgctgcttgt tcatcttttc gttttctccg ttctgtctgt catctgcgtt gtgtgattat
      601 atcgcgtacc acttttcgac tgttttaccg ccggtattct gccgtctgac gctttgacgg
      661 gtatttctgc ctgacaatac tgtcactgcc aaaaaactgc cgtgcctttg tcggtaattc
      721 gagcttgctg acaggacagg atgtgcaatt gttataccgc gcatacatgc acgctattac
      781 aattaccctg gtcagggctt cgccccgaca ccccatgtca gatacggagc catgttttat
      841 gacaaaacga agtggaagta atacgcgcag gcgggctatc agtcgccctg ttcgtctgac
      901 ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa tgcggcaaga ccgtttctgg
      961 ttttttacgg gcggcagctc tcggtaagaa agttaactca ctgactgatg accgggtgct
     1021 gaaagaagtt atgcgactgg gggcgttgca gaaaaaactc tttatcgacg gcaagcgtgt
     1081 cggggacaga gagtatgcgg aggtgctgat cgctattacg gagtatcacc gtgccctgtt
     1141 atccaggctt atggcagatt aacttcccgg agagaaactg tcgaaaacag acggtatgaa
     1201 cgccgtaagc ccccaaaccg atcgccattc actttcatgc atagctatgc agtgagctga
     1261 aagcgatcct gacgcatttt tccggtttac cccggggaaa acatctcttt ttgcggtgtc
     1321 tgcgtcagaa tcgcgttcag cgcgttttgg cggtgcgcgt aatgagacgt tatggtaaat
     1381 gtcttctggc ttgatattat attggaatgc cttttttcaa agcaaatgat gtggctttgg
     1441 atagaaggtt tacgttgatc ttatcaaagt tttttttaaa gaacgaagcc gagagctcag
     1501 ataaatcatt atattcatca gttttcgtaa ctttgtttaa tgtgtaactt gaaaacttct
     1561 cgccattaaa tgacgtatag acgtaacgat ctttttttcc accgttagga attattaaat
     1621 caaaaaaaac atcacccttg cttttctttt tcttcaagtc ggattcgatt tttgagaaaa
     1681 attcgctcgg gctataaata tcagtagcat agacaataaa taaagtttta tctttatttt
     1741 ttattgcttc tatttgatat tttttatctt ttttcataat ttcaacctag ctacgccacc
     1801 atctattaat tggcaaacgg tatcgatgat tgcgattgat tctaatttgt taattgtctt
     1861 cgtgtcagct attcctggtt tcatatgaaa caaaccatgc ctgttctcat gccagtaagt
     1921 gtagcattca cacaaaactt ccgctatttc accatttata gtttctcggt gtatttctct
     1981 gattatatat ttgggtttgt tttcagtgaa gtattcgcca aggttctttg atgatgatgg
     2041 attgcaaaca tcattaagta tttgatatat aaagccttct atggctctta atgcagagaa
     2101 gcagtatgtt gagtaatctt ccatttcgac atctattttt ttcattatta gcgagcatga
     2161 tagctgtttt ttgatatctt catggatttt atcgatgctt tttggtagtt tgctatgcaa
     2221 ctcggactca atagtttctt tttttatgtc aacattaaat tctttatttt tttgttcgac
     2281 aatctctttc atgtttagta ttgagcacat gaaatcgtta atcaaactcg cgatttgaag
     2341 gtattttcct tggaattgaa tagagccgcg cttgtaaatt tttgccctga ccctgtcacc
     2401 attgctggtg gtcataatat attggtgttt acaattagga tcgttattat tatcttctgt
     2461 tattgttatc ccctcttcag aaagaaattc aaatagattt gccctgtcat catcactgaa
     2521 ttttggaatg gtgtattcaa agttctttgt gtctgaatac aaacagtttt cttttataat
     2581 caaggcgatt tcatcaaagt aagtgttatt ttgcccagac gctcttccga tagtggtatt
     2641 tccgcctgat ggcattagtt ttattaagaa gtctattcct ttatatgtgc cagatatgtg
     2701 agtttctctt tcgtttttta cattagagga atagtttgtg acgccattct gcgtcagagc
     2761 agactcaatc ttgtcaatat tgatatttag tgctttaaac gggttctgtg ccattgggtc
     2821 aatccgttgt tttttttgaa tatgtacaga tcttgttttt ttgtcaacgg aatagctgtt
     2881 cgttgacttg atagaccgat tgattcatca tctcataaat aaagaaaaac caccgctacc
     2941 aacggtggtt ttctcaaggt tcgctgagct accaactctt tgaaccaagg taactggctt
     3001 ggaggagcgc agtcaccaaa atttgttctt tcagtttagc cttaacaggt gcataacttc
     3061 aagacaaact cctctaaatc agttaccaat ggctgctgcc agtggcgata agtcgtgtct
     3121 taccgggttg gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg
     3181 gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga gataccaaca
     3241 gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt
     3301 aagcggcagg gtcggaaca
//
