LOCUS       NZ_CP069888             4104 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1289 plasmid unnamed6.
ACCESSION   NZ_CP069888
VERSION     NZ_CP069888.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357431
            Assembly: GCF_016903315.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4104)
  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  JOURNAL   Unpublished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 4104)
  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                   :: 1351.18x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:17:14
            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)                     :: 5,431
            CDSs (total)                      :: 5,308
            Genes (coding)                    :: 5,115
            CDSs (with protein)               :: 5,115
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 193
            CDSs (without protein)            :: 193
            Pseudo Genes (ambiguous residues) :: 0 of 193
            Pseudo Genes (frameshifted)       :: 64 of 193
            Pseudo Genes (incomplete)         :: 139 of 193
            Pseudo Genes (internal stop)      :: 44 of 193
            Pseudo Genes (multiple problems)  :: 46 of 193
            Pseudo Genes (short protein)      :: 4 of 193
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069888.1.
            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..4104
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1289"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1289"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(146..400)
                     /gene="mobC"
                     /locus_tag="I6K19_RS26815"
                     /old_locus_tag="I6K19_26810"
     CDS             complement(146..400)
                     /gene="mobC"
                     /locus_tag="I6K19_RS26815"
                     /old_locus_tag="I6K19_26810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_204606483.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKGVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            579..2738
                     /gene="mobQ"
                     /locus_tag="I6K19_RS26820"
                     /old_locus_tag="I6K19_26815"
     CDS             579..2738
                     /gene="mobQ"
                     /locus_tag="I6K19_RS26820"
                     /old_locus_tag="I6K19_26815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2994..3686)
                     /locus_tag="I6K19_RS26825"
                     /old_locus_tag="I6K19_26820"
     CDS             complement(2994..3686)
                     /locus_tag="I6K19_RS26825"
                     /old_locus_tag="I6K19_26820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            3896..>4104
                     /locus_tag="I6K19_RS26830"
                     /old_locus_tag="I6K19_26825"
                     /pseudo=""
     CDS             3896..>4104
                     /locus_tag="I6K19_RS26830"
                     /old_locus_tag="I6K19_26825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001322464.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(402..578)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          579..937
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          complement(2995..3686)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          493..2735
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tccagtattc atgcgggttc agcgcatatc acctaccgaa aaaccgtgcg tatgtgctca
       61 acctggcgac ggattcactt ccgcttcctc gcccactcgc tcgctaacgc tcggtcgctg
      121 gggctgcggc gagcggacga tacaatcact gtcctggcag cgcctccagc tcgttaatca
      181 gcggcagtat gcgcgtcaca tcagcctgtc gtgtcacctc tgccttcagg aactggagta
      241 accaggcacg caactgcacc tcctccggct ttctgacctt tgccagcaat gctgcaccca
      301 caacaccctt ctgcgctgtg tccaggctcc ggctcttcgc cttcaggcgc tgtaatctcg
      361 cctcagcatc agcaatcttc tgttcgagcg ttctgctcat gatgtaactc cgtgcgcgat
      421 gaaaaatcgc attttagcgc gtcactggta gtttaaaaac tgagctggca taatgcgcga
      481 caaatcacaa agtgcgcact tatacaatct ccactccgtt tcgattgtgt gcgccctgcg
      541 gggctgaaag aaaactacaa aaaggcatta cggcagaaat ggcgatttat catctcagca
      601 tgaaaattat ctccagaagc agcggctaca gcgccgtagc ttccgctgcc tatcgttccg
      661 gttcactgat gcttgatgag cgtaccggac tgactcacga ctacacccgc aaaagcggtg
      721 tggctgaagc tgtgattctg acccccgcga cagcccctgc ctggtgtacg aaccgtgccg
      781 aactctggaa tgccgttgag aaggccgaat gccggaagaa ctcacaactt gcgcgggaaa
      841 ttgaactcgc tatcccccgt gaactgccgc aggatgccgc acgggaaacc gttctcgcct
      901 ttgtcagaga aaactttgtc agtcagggca tgattgctga tgtggcgttc catcacatgg
      961 ataaaacaaa tccccatgcg cacatcatgc tgaccacgag ggctgtcgga cctgctgggt
     1021 tcggcggaaa ggtcagggac tggaacgacc ggacacatgc cgagacgtgg cgtgcatcat
     1081 gggctgacca tgcaaacaga gcactggcga acgccggtta tcaggaagag atagaccatc
     1141 gttcatacga gcgacagggg cttgagaaaa cgcctggtat tcacctcgga aagtctgcct
     1201 gtgcgatgga aacacgcggt atcgaaacag aacgcggcga acagaatcgt ctgattaaca
     1261 ggcttaacct ggaaatacag atttcccgca ctgaactcag gaacagcggg ctgacagagc
     1321 ctgcccgccg tgtggctgac cttctgaata tcgtgcttcc tgacaacgca acttcgtaca
     1381 cactacgtga catcatcgaa gcgttgccga aggacagtaa tgcggcatgg aaactcacca
     1441 gtaatgccat gtcgatgatg gcagatatgc aggcgacgcg cagacgctgg gaagagctga
     1501 acaccgaacg aaaggaagcg atgagccatg ctgccagcct gaaaaaatca tcgccgtttt
     1561 cgtccggttt ttcccgtatt cccctgatgc aatgggcggc accggaatac cgtagcgaac
     1621 agggaaaaat ccagtcgctg agccagcaaa tggaaaaatt gcgacagcat taccggaagg
     1681 tggagaaaca ggacattccc gcgagtcaga cggcatttga aaaacagtgg cagcagtggg
     1741 gggcatccgg ccttgcagct ctcagagtcc agttgcttaa acgtgaagag gaattgcgcc
     1801 ggaaggagca ggaggataca gaacgtagtc gcgcggagcg acgagcggaa cagctcagga
     1861 aaaatgacaa tgccgttatg gattcagggg tactgagcgc agtcgttacg gggtatggcg
     1921 aggcccccat gcctggtaac ggggaaatga cctgttacct tctgcttcac aaccggaacg
     1981 gagaatacac gctctggggg aacgagctgg agaaataccg caccagaatc tttgagcgtg
     2041 ttgatttaat gcgtgacagg agtggttata tctgtgaccg aagcgaaatc ggtcaacatc
     2101 caccactgca acgtgtttat tcctctgcga cctttgagca acttctgacg caggtttgcc
     2161 agacatggcc gcaatatacc cgcaatctcc gccagccgaa gacatggccg gagtctttct
     2221 gtcttggaga agaccgccag ccagccatgc catcactggc agcaaggaag gtggatttta
     2281 cgcagggacg tctgctaccg acgctgatgc cggtaatgag ttctgtcgac cgggaaaccc
     2341 gccagcttca gcttttgctg gtcatgggcg tggatgactc tctgggcggt gttgtccggc
     2401 ttaatggtac gctgtatccc gcgtttgccg ttccctcagc cgataacagc cagctggtca
     2461 tcagtgcact gaccgataag gggttacggt atgcagggta tggtgttgcc gtaaatcacg
     2521 atgcagacag ccacatatca cctgcgccgg aacttatgga gtttcatctg aaaacccgtg
     2581 aggcaccgct ttttgctgcc gtcaacacac cagaaaaaca gccggatcat ctgttccgct
     2641 ctctgggttt caatcgtacc tgggatgaat ggcggcgcga ggaagatgca agaacacaca
     2701 ccaccgagag gagacatgat cgcggttggt cacagtgaat gtgaacaata ttttgttttg
     2761 tttaacatcg tgttatgttc gtcgatgttc ttctatgttc atcgacaggg atgaatgcaa
     2821 gaagcacaca cataatgcaa gcatagtttt gtttttccgc ccccaaaaat tgggggttct
     2881 tttttcgctg cattagagcg cttttgacgc aatttttcac ttcaatagta ccttcgcact
     2941 actaacacaa aaaaaacgca gcagggagcg ttttaggtgc cttaaaatcg attttagatc
     3001 gtcatcttga tctgtttgtc ttccttgaag cgaaaatgca gggctacaac cgtgcgcccc
     3061 tttttgatcg tctcaaccgt tacagccagg tcgctttttt tgttcagttc gtcaacacag
     3121 ggttttatta gtattttatt taagtctctg aattgtttgt atttattttc aatccctaac
     3181 attgaacgaa agtcattaag agcaataatt ctctctcccg tactgcggaa ttgctggagg
     3241 aactcgtata ttcttatact gtaactactt gataaacctg atatgttttt tataacaacg
     3301 cgcgtgaatt gccccttcag ttgcgtcaga taaggcatta ccgcgtcaga aaaggttatt
     3361 cgagccttgg cctcaccttt agcgtactgt gcccgatact ggatccagcg gaactcctca
     3421 cgcttctcgt cattcttgag aatgatcgac ctgtcccata aacgatcgat cgcttcctgt
     3481 aactgaacct cggcattttt ccgccccatg tcagggaatg aatcaaaata ttccgcagcg
     3541 gtaatggtca ttgtcttttg caattcagca tcagcaccag atttcaatcg actgatacac
     3601 agcaacagaa aacgttgttc ctgtagggtc aacttgtagc tggcctcaac caaagcattc
     3661 gacttgtagg caatcaagtc cgacatacaa agatcccgtt caaatgtggt gatgctttaa
     3721 tgtgccccac aaataagaaa tgtggaatat ttttttttat atcctcacat ttctgtgaat
     3781 aacaccttaa attcctccac ctttacctta aattcctcca cctaaacacc ttaaattcct
     3841 ccacctttac cttaaattcc tccacatata cctctataac atattgattt tattaatgaa
     3901 ttttgaccct aaaacaagta ttaaaaacaa gatcttaaaa acaagatcta aaaacttaac
     3961 ggcgagcctg tggataactt ggggcgctga aaacaaaaaa ccaataaaaa caatgtgttg
     4021 caagaaagca gaattgcaag ttccgaatac tccccttcca accctgtgga aatccattat
     4081 tcatgcgggg tcagcgcgta tcac
//
