LOCUS       NZ_CP069868             5631 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1282 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP069868
VERSION     NZ_CP069868.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357424
            Assembly: GCF_016903275.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  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  JOURNAL   Unpublished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 5631)
  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                   :: 976.61x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:21:51
            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)                     :: 5,162
            CDSs (total)                      :: 5,038
            Genes (coding)                    :: 4,852
            CDSs (with protein)               :: 4,852
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 186
            CDSs (without protein)            :: 186
            Pseudo Genes (ambiguous residues) :: 0 of 186
            Pseudo Genes (frameshifted)       :: 65 of 186
            Pseudo Genes (incomplete)         :: 127 of 186
            Pseudo Genes (internal stop)      :: 33 of 186
            Pseudo Genes (multiple problems)  :: 37 of 186
            Pseudo Genes (short protein)      :: 4 of 186
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069868.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1282"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1282"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(159..482)
                     /locus_tag="I6K12_RS25450"
                     /old_locus_tag="I6K12_25455"
     CDS             complement(159..482)
                     /locus_tag="I6K12_RS25450"
                     /old_locus_tag="I6K12_25455"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            547..738
                     /locus_tag="I6K12_RS25455"
                     /old_locus_tag="I6K12_25460"
     CDS             547..738
                     /locus_tag="I6K12_RS25455"
                     /old_locus_tag="I6K12_25460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1941..2807)
                     /locus_tag="I6K12_RS25460"
                     /old_locus_tag="I6K12_25465"
     CDS             complement(1941..2807)
                     /locus_tag="I6K12_RS25460"
                     /old_locus_tag="I6K12_25465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(2809..3861)
                     /locus_tag="I6K12_RS25465"
                     /old_locus_tag="I6K12_25470"
     CDS             complement(2809..3861)
                     /locus_tag="I6K12_RS25465"
                     /old_locus_tag="I6K12_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(4342..4575)
                     /locus_tag="I6K12_RS25470"
                     /old_locus_tag="I6K12_25475"
     CDS             complement(4342..4575)
                     /locus_tag="I6K12_RS25470"
                     /old_locus_tag="I6K12_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4582..5112)
                     /locus_tag="I6K12_RS25475"
                     /old_locus_tag="I6K12_25480"
     CDS             complement(4582..5112)
                     /locus_tag="I6K12_RS25475"
                     /old_locus_tag="I6K12_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<5150..5581)
                     /locus_tag="I6K12_RS25930"
                     /pseudo=""
     CDS             complement(<5150..5581)
                     /locus_tag="I6K12_RS25930"
                     /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"
     Typing          complement(833..914)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(1371..1558)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(163..515)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.458"
                     /coverage="100.0"
                     /evalue="3.2e-69"
     Typing          complement(4239..5629)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cacctgacgt gtatttcttc gcaaatggcg tggcatcgat gagttcccgg acctcttccg
       61 gattcccctg aagcaccgtt gccccttccc ggttacgctc ccttcccagc aggtaatcaa
      121 ccggaccact gccaccacct tttcccctgg catgaaactt aactatcatc ccgcgccccc
      181 tgttccctga ccgccagacg cagccggcgc agctcatccc cgatggccat cagtgcggcc
      241 accacctgaa cccggtcacc ggaagaccac tgcccgctgt tcaccttcct cgctgtctgg
      301 ttaaggttat tcccgatggc ggccagctga cgcagtaacg gcggtgccag tgtcggcagc
      361 ttcccggaac gggcaaccgg ctcacccagg cagacccgcc gcatccatac cgccagttgt
      421 ttaccctcac agcgttccag taaccgggca tgttcatcat cagtaacccg tatcgtgagc
      481 atcctctcgc gtttcatcgg tatcattacc cccatgaaca gaaccccccc ttacacggag
      541 gcatcagtga ccaaacagga aaaaaccgcc cttaacatgg cccgcttcat cagaggccag
      601 acattaacgc tgctggagaa gctcaacgaa ctggacgcgg atgaacaggc agacatctgt
      661 gaatcgcttc acgaccacgc cgatgagctt taccgcagtt gcctcgcacg cttcggggat
      721 gacggtgaaa accgctgaca catgcagctc ccggagacgg tcacagcttg tctgtgagcg
      781 gatgccggga gcagacaagc ccgccagggc gcgtcaggcc gttgaccttt ggggtgtcgg
      841 ggcgaagccc tgacccagtc acgtagcgat agcggagtgt atactggctt aaccattcgg
      901 catcagtgcg gattgtatga aaagtgcgcc atgtccggtg tgaaatgccg cacagatgcg
      961 taaggagaaa atgccagttc aggcgctctt ccgcttcctc gctcactgac tcgctacgct
     1021 cggtcgttcg gctgcggcga gcggactctc ctttctcaaa aacgctaacc ctgttatcca
     1081 cagaacccgg ggataaacca ggaaagaaca tgtgcgcaaa aaacgaaacc ccgggaaagg
     1141 ccgcgccgga ggcgcttttt ccataggctc cgcccccctg acggacttca caaaacagac
     1201 actttttcgg tgcatctgtg ggagccttgc ggctcaacca tgaaatccgc cagcggtggc
     1261 gaaacccgac gtggcttaaa gatcatcacc gtttccggtg aatcgctccc tcctgcgccc
     1321 ccacgttccc gccatatcga ttaccggata ccttttccgc ctttctccct tacgggacac
     1381 gtggcgcttt ctcatagctc acgtcttctg gtatctcggg gcgacttagg cagttcgctc
     1441 cgggctgggc tgtatgcagg aaccccccgt tcagcccgac tgctgcgcct tctccggtaa
     1501 ctgttctctt gggtccaacc cggaaaagac accacaaagc gccactggca gcagccattg
     1561 gtaaaagtca tgtgcgagat atttagagag tacttgaagt ggctgccgga gtgcggctac
     1621 actagaagaa caattttggt gactcgtctc gcataagaca gttacctggt taagcagtct
     1681 gcaagctgac ttaaccttcg atcaaaccgc cctgcaaggc ggttttttcg tttacaggca
     1741 gcagattacg cgcagaaaaa aaggatctca agaggatcct ttgatctttt tgttacaaac
     1801 gtctctattt gactcccctg agagcgtttt agcgcgcctc tgaccccctt ggttacattc
     1861 cgacaccaga aacgctcccg ttttttacgt gcatttggca cggtatcgat ggaggccggg
     1921 gggcaatcct gaacagaatg ttactcctct gagtattttc tgttaagaaa atatacactt
     1981 agcacagtta caataaatcc taccccctgt aagaatgtga attgttcatc caaaaacaac
     2041 catgacaaaa ataatgcaac tagcggaata aagtacaaca ttatccctgc caaatgaact
     2101 gggagccaac gcaaggagtt caagtaaaaa caaaaagcta aaaaatattg taatattcca
     2161 gatgaaaaaa caataatcac ggattccaac ggaagataaa ttgatgattt agatataaaa
     2221 ataaagagcg atgacagtat aagggagaat gtcaactgtc cgctcaataa tgtgataggc
     2281 tcaaacgatt taataaggcg agacgatata acaacataaa atgctgccga taacacaccg
     2341 gcaacaacaa gacaatatcc aacaatatta ttcgatccat tactgatgtc tggcaaggct
     2401 accaaaatac tgccaacaat tgcacctata aggaacaata taaaatattg cggggaatta
     2461 attttaactg agcaaataag aacagacaac accaatataa acactgattc aagtgaaaaa
     2521 ataattgatg cgcttcctgc tgaaataaaa taaagtccgt agagtgtaaa agtatacgct
     2581 aagaatggtt caaaaacgcc tgtcgcataa gcaagtatcg cttttgagtt taatgggagt
     2641 ttttttcttt ttataaaaag aactatccaa gatagtatta ctgcactaca aatctgccag
     2701 aaaaacaccc ctccggcatc tagttcttca actccttttt tgctcattac gatagctgcc
     2761 ccccatgaga acgctgctaa aaaagcaaaa agcattcctt taatcatatt aatcatcctc
     2821 tttctcataa aggggtttgt tttcaaattt ccttggttga aaggagttaa aaaacataga
     2881 tgcatcatct acaggaatac caataaactc tccataataa ggatcatcta taggaaactc
     2941 ttctaatgaa acataaaaca atacattcca gttgaagatc attggatcac tattttctat
     3001 ttcatggagc aatctttcat ccttagttaa ttctcctgga attaatacat cagtatgata
     3061 aaaaccgctg taataagaac tattaccggt gtgcactggg catccaaaac gatccaaatt
     3121 agattctgaa tgccatgttg tagaaatccc ttccggatgt gaatacccac ccttaccaac
     3181 agactgaata gtcatgttac gaatatccgc taacgcttgt tcttgatctt tatagaaacc
     3241 tttttctatc gccagcctca taaaatgccc cggggcattt acagaaataa gtattccccc
     3301 tggtattctt ctatcatgat ttcttgttct atgagcagaa gagtaaaaaa cattaacacc
     3361 agccttatat atttttagcc catctttatc ctgaaatggt acgctttcag tataaataac
     3421 atcctctttt attggatagc actctggcat atgcagcgaa caaatatatt tttgtatgtc
     3481 cactaactct tctgatggac gagcaaaggc aagttgtgga tgaataaaat aaatgagatg
     3541 cgcactgacc tctcctcttc ttgcgcgttc tttaaaacga actctttcat tacgcaaaaa
     3601 atcaaacaaa tgaccatcat cattatatag ttgggggcta tttacaatag ataaatggaa
     3661 atcaagccct ttaattttct tgcttgccaa tttaccaaat acacagggct gattgcctga
     3721 cacccatttt cttagtaaat cttcaatttt atctttagaa gtttcgttaa agataaatga
     3781 atgaatatta tcaatatctt ttccaaatga aaaactggat gataattgtg gtagtttatt
     3841 tatacgttgt tgaagattca tgaaagctcc cacaagacac ctcatatatt tttttatata
     3901 ctgaaactac attatattta ttaccggcgt aaaacgaaat aatttattat cgttaccgat
     3961 attttaaaaa aatcattatt tgcacagtgt tcgagttgtt agtatcactc cttcctgaaa
     4021 atccgctcca tttaccataa cgtcgcattg tacgcaccgc caaaacgcgt tcggtgcgat
     4081 cacggcagca gacaggtaaa aatggcaaca aaccacccga aaaactgccg cgatcgcacc
     4141 tgataaattt taaccgcatg aatacctatg caaccagatg ctacaggcca cattagcccg
     4201 ccttaatcca ctgaacacgt catttttcat ggtttcacca tcccagcgaa gggccatcca
     4261 gtgtccgctc ctggatttcc ggctgacgct cccgctccag agataactca tgttcgcgtt
     4321 cctgcatcag ccgttcatcc cttatctcct gttctcgctg tataactggc tcaagcgttc
     4381 tgtccgctcg ctcaagtgct gcacctgctg actcaactgc atgactcgcc cgttcagcat
     4441 cgcgttgtcc cgttgcgtaa gcgaaaacat tttctgcaat tccacgaagg cgttctccca
     4501 ttcgttcagc cgctgcatat agtcctgttg cagttgctct aatgcgttca gcaaatgtct
     4561 ttccagctcc gtcatgctct gtcactcctg caccagtctc actgcgttca gtttgccgtt
     4621 gtccttcgtc cagttcgttt cggctttcat ccccttcggc aacaccagaa aacgtccgtt
     4681 gctgtcctcg tgataacgca cgccccatgt cttcgcgttc agcttctcca gactctcttt
     4741 ctgctcgcgg agaatattca tattcgcgtt tatcttcatg ccctggtacc acagcagact
     4801 cccggtcgtg gcaaacatca gtactgagac gataatcagc cacagccagc gtttcacgct
     4861 cattttcagt acggttttcc agtgcgcgtc catcgtatcg acggtcgttt tctgatacct
     4921 ctccagcagt tctttcaggg ctgttgtatg gtcgttgata gcgttcctga ttaaagattc
     4981 gtttgaggtc agttccctgt ttacagattc ttcgagcttc ctgaactcgt cgttcagcat
     5041 tttctctgta gattcggctc tctctttcag ctttttctcg aactccgcgc ccgtctgtaa
     5101 aagattgctc ataaaacgct cctttcagtc tgatattcct cccgccgttc gggtctgcaa
     5161 tgctgatact gcttcgcgtc accctgacca cttcaagccc cgcctctgtg agcgcctgaa
     5221 tcacatcctg acggcctttt atctctccgg catggtaaag cgcgtctatc ccgcgtgtga
     5281 cgccctcagc aagcgcctgt ttcgtttccg gcaggttatc aggaagggtc agcgtccggc
     5341 ggttctccgg ggcgttgggg tcatgcagac cgtaatggtg attcaccagc gtctgccagg
     5401 catcaattct cggcctgtct gcccggtcgt agtacggctg gaggcgtttt ccggtctgta
     5461 gctccatgtt cggaatgaca aaattcagct caagccgtcc cttgtcctgg tgctccaccc
     5521 acaggatgct gtactgattt ttctcgagac cgggcatcag tacacgctca aagctcgcca
     5581 tcactttttc acgccctcca ggcggcagct ccttctccgc gaacgacaga a
//
