LOCUS       NZ_CP069574             3360 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1250 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP069574
VERSION     NZ_CP069574.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357392
            Assembly: GCF_016890005.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3360)
  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  JOURNAL   Unpublished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 3360)
  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, SPAdes v. 3.14.1
            Genome Coverage                   :: 770.24x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:03:03
            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)                     :: 5,029
            CDSs (total)                      :: 4,910
            Genes (coding)                    :: 4,669
            CDSs (with protein)               :: 4,669
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 241
            CDSs (without protein)            :: 241
            Pseudo Genes (ambiguous residues) :: 0 of 241
            Pseudo Genes (frameshifted)       :: 65 of 241
            Pseudo Genes (incomplete)         :: 178 of 241
            Pseudo Genes (internal stop)      :: 44 of 241
            Pseudo Genes (multiple problems)  :: 45 of 241
            Pseudo Genes (short protein)      :: 4 of 241
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069574.1.
            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..3360
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1250"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1250"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            join(3347..3360,1..220)
                     /locus_tag="I6J80_RS24700"
                     /old_locus_tag="I6J80_24710"
     CDS             join(3347..3360,1..220)
                     /locus_tag="I6J80_RS24700"
                     /old_locus_tag="I6J80_24710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1524..1715)
                     /locus_tag="I6J80_RS24705"
                     /old_locus_tag="I6J80_24715"
     CDS             complement(1524..1715)
                     /locus_tag="I6J80_RS24705"
                     /old_locus_tag="I6J80_24715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1779..2102
                     /locus_tag="I6J80_RS24710"
                     /old_locus_tag="I6J80_24720"
     CDS             1779..2102
                     /locus_tag="I6J80_RS24710"
                     /old_locus_tag="I6J80_24720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2311..>2751
                     /locus_tag="I6J80_RS25225"
                     /pseudo=""
     CDS             2311..>2751
                     /locus_tag="I6J80_RS25225"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2780..3340
                     /locus_tag="I6J80_RS24720"
                     /old_locus_tag="I6J80_24730"
     CDS             2780..3340
                     /locus_tag="I6J80_RS24720"
                     /old_locus_tag="I6J80_24730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     Typing          1360..1443
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          2093..3360
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.69"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agggcatttg ctgaacgcct tagagcattt gcaacaggac tatatgcggc ggctgaacga
       61 gtgggagagc gccttcgcgg aattgcagaa gatgcacgag gttacgcaac ggaacaacgc
      121 gatactgaac gagcgcgtcg tgatattgag tcagcaggtg cagagattag ccgggcaagt
      181 ggatcgcttg agtcggttat ttatcgcgaa caacagctaa gggatgaaca ggagcgtgcc
      241 cggtacagac atgaggtaca ggaacgcgcg gcacgggttc ggagtgggcc atcaatggag
      301 atgtgacgaa atcttgccat tttgaccagt tcgacggctg gggcgagcga aacaaatcgt
      361 gtgccgtatt tgtgcatagc tatgcaacat cctgaaaacg catttcacgc gtttttgggg
      421 attcagccag gggaaaacat ggttttttta ctttttgagc gtaaagacgt gaaaaatctc
      481 gttattgcac ttgcgatctt tcgtcggcgg gagtagaacg aaaacagctc gccaggaagg
      541 cgagctgttt cgggttcatt gaggtctctg acctcctcaa tgttcctgtg gaaactgttg
      601 agatccacaa cagaaaccag ttcattcagt ttgcatgagc cttctgtatt cttcaagaat
      661 ttttcaacag cacagtctcc caggaacccc gaaaaaaacc tgtttttgca gatacttgcg
      721 tatttgcgag aatcgtttgc ggttggggga gctgtgacga cggcgaccgc acgcgtgaga
      781 gttccgctac cggcgcagag agtttcatcg acagcggaca cctgatgagt tgccacaaaa
      841 accgtatgta gcgcggctag attggttgag ttagaccttg gcggcagttc ccggtatgtg
      901 gtggcgtgac gggtgagatg gtgcggcgaa gacgcatacg tcacgcaggc gcgggttctt
      961 ccactgacgc gccccgtgat cgatggcctt ggctccgtcc ggcatatcga gagcggcaaa
     1021 ctacccgtcc cttcactggg aggggtgagt tgttgccgtt ccctccaacc tttcaccatc
     1081 cggcatatcg cacgatccca tgtgcaccgc aactcctgat aactccagtg caaaaaaaaa
     1141 aaacggatct gcatcacaac gagagtgatc ccaccgctcg ccgcagcccc agcgaccgaa
     1201 cgtagtgagc gagtgggcga ggaagcggaa gagtcacaga tgcaagcatt gtgcacttac
     1261 gcgcctgtga cagtgtccgc gtgtgtgctg tttatcgggt gcgctgtttt tacatctgtg
     1321 cggcttttta ctcctgacat ggtgcacttc ccatccactc tgcaccgatg caaaatgaga
     1381 taagccagta tacacatcgc tatcgctctg tgaactgggt cagggctgcg ccccgacacc
     1441 cgcactgacg cgccctggcg ggcttgtctg ctcccggcat ccgctcacag gcaagctgtg
     1501 aacgtctccg ggagctgcat gtttcagttg ctttcaccgt catcgccgaa gcgtgcgagg
     1561 caactgcggt agagttcgtc ggcgtggtcg tgaagtgatt cgcagatgtc tgcctgttcg
     1621 tccgcgtcca gatcgttgag tttttccagc agggttagcg tctggcttct gataaagcga
     1681 gccatgttaa gggctgtttt ttcctgtttg gtcatggtct taaggctcct tgtatggggg
     1741 atttgttagg gggaatgata ccgatgaaac gcgagaagat gctcacgata cgggttaccg
     1801 atgaggagca cgcccggtta ctggaacgct gcgagggtaa acgactggcg gaatggatgc
     1861 ggcgggtctg tctgggggag ccggttgcac gcacaggaaa actgccgaca ctatcgccgc
     1921 cattgctgcg gcatctggct gccatcggga acaacctgaa ccagacagcc cggaaggtga
     1981 acagcggtca gtggtcttcg attgaccggg ttcatgtggt ggccgcactg atggccatcg
     2041 agggtgaatt gcgccagttg cggcaggctg tcagggaaca gggggtacgg gatgatagtt
     2101 aaatttcatg ccagggggaa aggcggtgga agtggcccgg tcgattacct gctggggcgg
     2161 gagcgtaacc gcgaaggcgc aacggtgctc cggggtaacc cggaagaagt gcgagaactc
     2221 attgattcca cgccattttc gaagaaatac acttcaggcg ttctgtcgtt cgcggagaag
     2281 gagttaccgc cgggtgaacg cgaaagagtg atgacgagct ttgagcgtgt tcttatgccc
     2341 ggtctcgaaa aagaccagta cagcattctc tgggtggaac accaggataa ggggcggctc
     2401 gaactgaatt ttgtcatccc gaacatggag ctacagagcg gtaagcgcct ccagccgtac
     2461 tacgaccgcg cggacaggcc gaggataaat gcctggcaga cgctggttaa tcatcattac
     2521 gggctgcgtg acccgaacgc accggagaac agacggacgc ttgtcacgcc aaataatctg
     2581 ccaaaagcga aacaggaggc cgcagaagcg attacacggg gtcttgaggc tctttaccat
     2641 gccggagcaa taaaaacgcg tcaggatgtc acagaggcgc ttacagcggc aggttttgag
     2701 gtggtgagga caaccaaaag cagcatcagt attgccgacc cggagggggg gcggaatctc
     2761 aggctaaagg gggcgctgta tgagcaatct tttacaaatg ggaacagact tcgagaagaa
     2821 actgaaagag cgagccgctt ctaccgagaa catgctgaac agcgagttca ggaagctcga
     2881 agagtctgta gacaaggcat tgagcttaaa caggcagaaa atcagagacg ctatcagcga
     2941 acatacaaca tccgtgaaaa agcaactgga tacgctgagc accaccgtga gcatgcagtt
     3001 cagcaccaca gaggccgaac tgtcccggca gcagaaaaaa ctgctctggc gggtgatcaa
     3061 agggcggata ctgtttccgg cgctgaccgc gctcagcgtc acgggcggca ttttcctggg
     3121 gtgctggggg ctgatggagt ggcaggaaag caagattgcg aaaaatatcc tgactatcag
     3181 agagcaggaa aacacgctgg cgaaactcga ggcaaaaacc tggggggtga cgttcgtcaa
     3241 tggcgagaac gggaaatttc tggtgttgcc ggacggggtg aaaggggaaa acacctggac
     3301 ggtgggcgac aagaacgccg tgaggctggt cagggagtaa acgagtatga cggaactgga
//
