LOCUS       NZ_CP069547             3816 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1248 plasmid unnamed5.
ACCESSION   NZ_CP069547
VERSION     NZ_CP069547.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357390
            Assembly: GCF_016889845.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3816)
  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  JOURNAL   Unpublished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 3816)
  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                   :: 947.14x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:14:06
            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)                     :: 4,982
            CDSs (total)                      :: 4,860
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 68 of 240
            Pseudo Genes (incomplete)         :: 167 of 240
            Pseudo Genes (internal stop)      :: 52 of 240
            Pseudo Genes (multiple problems)  :: 43 of 240
            Pseudo Genes (short protein)      :: 4 of 240
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069547.1.
            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/
FEATURES             Location/Qualifiers
     source          1..3816
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1248"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1248"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(622..813)
                     /locus_tag="I6J78_RS24490"
                     /old_locus_tag="I6J78_24495"
     CDS             complement(622..813)
                     /locus_tag="I6J78_RS24490"
                     /old_locus_tag="I6J78_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165980.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADDQADICEALHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            881..1204
                     /locus_tag="I6J78_RS24495"
                     /old_locus_tag="I6J78_24500"
     CDS             881..1204
                     /locus_tag="I6J78_RS24495"
                     /old_locus_tag="I6J78_24500"
                     /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_001444404.1"
                     /translation="MLTIRVTDEEHARLLARCEGKQLASWMRKVCLGAPPSKTSGLPTL
                     APPLLRQFASVGNNLNQIARKINSGQWSGHDRVHVVAALMAIGRELSELRDEVRKQGER
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1413..>1850
                     /locus_tag="I6J78_RS24955"
                     /pseudo=""
     CDS             1413..>1850
                     /locus_tag="I6J78_RS24955"
                     /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            1882..2442
                     /locus_tag="I6J78_RS24505"
                     /old_locus_tag="I6J78_24510"
     CDS             1882..2442
                     /locus_tag="I6J78_RS24505"
                     /old_locus_tag="I6J78_24510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067489.1"
                     /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_000067489.1"
                     /translation="MSNLLQMGTDFEKKLKERAVSTENILNSEFRKLEASVDRELNLNG
                     QKIRDAISAHTAAVKEQLETLNSAVNAQFSATENELARRQEELLWKLVKGRILYPSLTA
                     LCVTGGIFLASWGLIQWQESRIAANILAIRDQEETLAKLREKTWGVTYHEGRNGKFLVL
                     PSGVKGENNWTVEKKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2449..2682
                     /locus_tag="I6J78_RS24510"
                     /old_locus_tag="I6J78_24515"
     CDS             2449..2682
                     /locus_tag="I6J78_RS24510"
                     /old_locus_tag="I6J78_24515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137429.1"
                     /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_000137427.1"
                     /translation="MTELEMHLLNALEQLQQDYTQRLKDWESAFTDLQHMFELTRQENG
                     QLREQCDDLSQQVQRLAGQVDHLSRLFITNSR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3176..>3816)
                     /locus_tag="I6J78_RS24515"
                     /old_locus_tag="I6J78_24520"
     CDS             complement(3176..>3816)
                     /locus_tag="I6J78_RS24515"
                     /old_locus_tag="I6J78_24520"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=3
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_204148186.1"
                     /translation="YLDDEIKSLKTVSFGDDHELRKLSHYLDDEIKSLKAVSFGDDHEL
                     RKLNRYLDDEIMSLKTVNFGDDLELRKLNRYLDDEIMSLKTVSFGDDHELLELNRYLDD
                     EIMSLKTVSFGDDHELRKLNRYLDDEIKSLKTVSFGNDHELRELNRYLDDEIMSLKTVS
                     FGNDHELLELNRYLDDEIKSLKTVSFGDDHELLELNRYLDNELRNLKIK"
                     /name="hypothetical protein"
     Typing          450..537
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.753"
                     /coverage="100.0"
                     /evalue="1.48e-35"
     Typing          1195..2789
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.248"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cggaactgag tgtcaggcgt ggaatgagaa accgcggcca taacagcgga atgacaccgg
       61 taaaccgaaa ggcaggaaca ggagagcgca cgagggagcc accaggggga aacgcctggt
      121 atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ttgtgatgct
      181 cgtcaggggg gcggagccta tggaaaaagc gcctgcggcg cggccttttt cggggtttcc
      241 gtttttgcgc acatgttctt tcccgggtta tccccggatt ctgtggatac tgtgttaccg
      301 tttttgtgtg agtcagtacc gctcgccgca gccgaacgac cgagcgtagc gagtcagtga
      361 gcgaggaagc ggaaaagcgc ctggacgtgc attttctcct tacgcatctg tgcggcattt
      421 cacacccggc atggagcact ttttatacaa tccgcactga tgccgcataa gtaagccagt
      481 atacactccg ctatcgctac gtgactgggt catggctgcg ccccgacacc cgctaaaacc
      541 tgctgacgcg ccctgacggg cttgtctgct cccggcatcc gctcacaggc cagctgtgac
      601 cgtctccggg agctgcatgt gtcagaggtt ttcaccatca tccccgaagc gtgcgaggca
      661 gctgcggtaa agctcgtcag cgtggtcgtg aagcgcttcg cagatgtcag cctggtcgtc
      721 ggcgtccagt tcattcagtt tttccagcag ggtcagcgtc tggcttctga tgaagcgggc
      781 catgttaagg gcggtttttt cctgtttagt cacagttctg tttctccatg tgtggggagt
      841 ctgtcggagg tttttaatga taccggtgaa acgcgaaagg atgctcacga tacgggtcac
      901 ggatgaggaa catgcgcggc tgctggcacg ttgtgaggga aaacaacttg cgtcatggat
      961 gcgtaaggtc tgcctggggg caccgccatc gaaaacgtca ggtcttccga cactggcacc
     1021 gccgctgttg cgccagttcg cttcggtcgg caataacctg aatcagatag cccggaagat
     1081 aaacagcgga cagtggtcgg ggcatgaccg ggttcatgtg gtggctgcac tgatggccat
     1141 cggacgtgaa ctgagtgagc tgagggatga ggtccgtaaa cagggagaac gggatgatag
     1201 ttaagtttca tgccagggga aaaggcggtg gcagtggtcc ggttgattac ctgctgggcc
     1261 gggagcgtaa ccgggaaggg gcgagagttc tgcggggtgc tcccgaagag gtgcgggaac
     1321 tcatcgatgc cacgccgttt gcgaaaaaat acacctcggg ggttctgtct tttgcagagc
     1381 agaccctgcc accgggagag cgtgaaaggg tgatggagag ctttgagcgg gtactgatgc
     1441 ccggtcttga aaaaaatcag tacagcatcc tgtgggtgga gcaccaggac aaggggcgtc
     1501 ttgagctgaa ttttgtcatc ccgaatatgg agctggcgag cggaaaacgg ctccagccct
     1561 attacgaccg agcggaccgt ccgcgaatca atgcctggca gacactggtg aatcaccatt
     1621 acgggctgca cgacccgaac gcaccggaga acaggcggac acttgtcacc ccgaataatc
     1681 tgccgaaagc gaaacaggag gccgcagaag cgattacgag gggactggag gctctttacc
     1741 atgccggagc gctaaaaacg cgtcaggatg tcactgaggc gcttacagcg gcaggttttg
     1801 aggttgtgag gacaaccagg agcagtatca gtatcgccga cccggagggc gggcgtaatc
     1861 tcaggctgaa aggggcgctg tatgagcaat cttttacaaa tggggacaga cttcgagaag
     1921 aaactgaaag agcgtgccgt ctctacagag aacatactga acagcgagtt caggaagctc
     1981 gaagcgtctg tagacaggga actgaactta aacgggcaga aaatcagaga cgctatcagc
     2041 gcacacacag cagcggtgaa agaacaactg gagacgctga acagtgccgt gaacgcgcag
     2101 ttcagcgcca cagagaacga actggcccgg cggcaggaag agctgctctg gaagctggtc
     2161 aaagggcgga tactgtaccc gtcgctgacg gcgctttgcg tcacgggcgg gatttttctg
     2221 gcgtcatggg ggctgattca gtggcaggaa agccggattg cggcgaacat cctggctatc
     2281 agggaccagg aagagacgct ggcgaaactc cgggaaaaaa catggggtgt gacgtatcac
     2341 gagggcagga acgggaaatt tctggtattg ccgtccgggg tgaaggggga aaacaactgg
     2401 acggtggaga agaagaacgc agtaagactg gtcagggagt aagtgagtat gacagagctg
     2461 gaaatgcact tactgaacgc cttagagcaa ttgcagcagg actatacgca gcggctgaaa
     2521 gactgggaga gcgccttcac ggatttgcag catatgttcg agctgacacg acaggagaac
     2581 gggcaactga gggaacagtg cgacgacttg agtcagcagg tgcagagatt agccgggcag
     2641 gtggaccact tgagtcggtt atttatcacg aacagcagat aagggatgaa caggaaaggc
     2701 aggcacgcct ggaacgggag cgtgcgcggt cctggcatga agagcaggaa cgggaagcac
     2761 gggtatggcg tggcccgtca ataggtatgt gacggtgagt tgttccggga ggttgccaga
     2821 tggtaccgga acgcgttaaa aacgcatccg ggcgcgattc tggcgtgtcg tttttgttgc
     2881 tgtgttttgc ctctttgcca gatcgcgctc attcctcagc ctcatcccgc gatgtctgcg
     2941 tatgtcatca actgaaaaga tggaaaaaaa acagtgtcat gaggtttacg caggcaaaac
     3001 cagcgttatt cacatggctg aatagctatg catacggtta aaatttatca ggtgcgatcg
     3061 cggcagcttt tcgggtggtt tgttgccatt tttacctgtc agcagccgtg atcgcgctga
     3121 acgcatttca gcggtgcgta caattggatg ttatggtaaa tggctctcgc tagtttcatt
     3181 taatttttaa attacgaagc tcattatcca gatagcgatt cagctcgagg agctcgtggt
     3241 catcgccgaa actgacggtt ttcaggctct tgatctcatc gtccagatag cggttcagct
     3301 cgaggagttc gtggtcattg ccgaaactga cggttttcag actcatgatc tcatcgtcca
     3361 gatagcggtt cagttcccgg agttcgtggt cattgccgaa actgacggtt ttcaggctct
     3421 tgatctcatc gtccagatag cggttcagtt tccggagctc gtggtcatcg ccgaaactga
     3481 cggttttcag actcatgatc tcatcgtcca gatagcggtt cagctcgagg agctcatggt
     3541 catcgccgaa actgacggtt ttcaggctca tgatctcatc gtccagatag cggttcagtt
     3601 tccggagctc gaggtcatcg ccgaaattga cggttttcag actcatgatc tcatcgtcca
     3661 gatagcggtt cagtttccgg agctcatggt catcgccgaa actgacggct ttcaggctct
     3721 tgatctcatc gtccagatag tggctcagtt tccggagttc gtggtcatcg ccgaaactga
     3781 cggttttcag gctcttgatc tcatcgtcca gatagc
//
