LOCUS       NZ_CP070167             5504 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1283 plasmid unnamed5.
ACCESSION   NZ_CP070167
VERSION     NZ_CP070167.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357425
            Assembly: GCF_016904615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5504)
  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  JOURNAL   Unpublished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 5504)
  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                   :: 868.58x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:33:33
            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)                     :: 5,127
            CDSs (total)                      :: 5,003
            Genes (coding)                    :: 4,791
            CDSs (with protein)               :: 4,791
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 96 of 212
            Pseudo Genes (incomplete)         :: 128 of 212
            Pseudo Genes (internal stop)      :: 49 of 212
            Pseudo Genes (multiple problems)  :: 52 of 212
            Pseudo Genes (short protein)      :: 3 of 212
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070167.1.
            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..5504
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1283"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1283"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            <1..117
                     /locus_tag="I6K13_RS25330"
                     /old_locus_tag="I6K13_25325"
     CDS             <1..117
                     /locus_tag="I6K13_RS25330"
                     /old_locus_tag="I6K13_25325"
                     /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_114138562.1"
                     /translation="LNELDADEQADICESLHDHADELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1320..2186)
                     /locus_tag="I6K13_RS25335"
                     /old_locus_tag="I6K13_25330"
     CDS             complement(1320..2186)
                     /locus_tag="I6K13_RS25335"
                     /old_locus_tag="I6K13_25330"
                     /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(2188..3240)
                     /locus_tag="I6K13_RS25340"
                     /old_locus_tag="I6K13_25335"
     CDS             complement(2188..3240)
                     /locus_tag="I6K13_RS25340"
                     /old_locus_tag="I6K13_25335"
                     /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(3721..3954)
                     /locus_tag="I6K13_RS25345"
                     /old_locus_tag="I6K13_25340"
     CDS             complement(3721..3954)
                     /locus_tag="I6K13_RS25345"
                     /old_locus_tag="I6K13_25340"
                     /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(3961..4491)
                     /locus_tag="I6K13_RS25350"
                     /old_locus_tag="I6K13_25345"
     CDS             complement(3961..4491)
                     /locus_tag="I6K13_RS25350"
                     /old_locus_tag="I6K13_25345"
                     /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(<4529..4960)
                     /locus_tag="I6K13_RS25790"
                     /pseudo=""
     CDS             complement(<4529..4960)
                     /locus_tag="I6K13_RS25790"
                     /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            complement(5169..5492)
                     /locus_tag="I6K13_RS25360"
                     /old_locus_tag="I6K13_25355"
     CDS             complement(5169..5492)
                     /locus_tag="I6K13_RS25360"
                     /old_locus_tag="I6K13_25355"
                     /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_125094207.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMIIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(212..293)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(750..937)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3618..5179)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcaacgaac tggacgcgga tgaacaggca gacatctgtg aatcgcttca cgaccacgcc
       61 gatgagcttt accgcagttg cctcgcacgc ttcggggatg acggtgaaaa ccgctgacac
      121 atgcagctcc cggagacggt cacagcttgt ctgtgagcgg atgccgggag cagacaagcc
      181 cgccagggcg cgtcaggccg ttgacctttg gggtgtcggg gcgaagccct gacccagtca
      241 cgtagcgata gcggagtgta tactggctta accattcggc atcagtgcgg attgtatgaa
      301 aagtgcgcca tgtccggtgt gaaatgccgc acagatgcgt aaggagaaaa tgccagttca
      361 ggcgctcttc cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag
      421 cggactctcc tttctcaaaa acgctaaccc tgttatccac agaacccggg gataaaccag
      481 gaaagaacat gtgcgcaaaa aacgaaaccc cgggaaaggc cgcgccggag gcgctttttc
      541 cataggctcc gcccccctga cggacttcac aaaacagaca ctttttcggt gcatctgtgg
      601 gagccttgcg gctcaaccat gaaatccgcc agcggtggcg aaacccgacg tggcttaaag
      661 atcatcaccg tttccggtga atcgctccct cctgcgcccc cacgttcccg ccatatcgat
      721 taccggatac cttttccgcc tttctccctt acgggacacg tggcgctttc tcatagctca
      781 cgtcttctgg tatctcgggg cgacttaggc agttcgctcc gggctgggct gtatgcagga
      841 accccccgtt cagcccgact gctgcgcctt ctccggtaac tgttctcttg ggtccaaccc
      901 ggaaaagaca ccacaaagcg ccactggcag cagccattgg taaaagtcat gtgcgagata
      961 tttagagagt acttgaagtg gctgccggag tgcggctaca ctagaagaac aattttggtg
     1021 actcgtctcg cataagacag ttacctggtt aagcagtctg caagctgact taaccttcga
     1081 tcaaaccgcc ctgcaaggcg gttttttcgt ttacaggcag cagattacgc gcagaaaaaa
     1141 aggatctcaa gaggatcctt tgatcttttt gttacaaacg tctctatttg actcccctga
     1201 gagcgtttta gcgcgcctct gacccccttg gttacattcc gacaccagaa acgctcccgt
     1261 tttttacgtg catttggcac ggtatcgatg gaggccgggg ggcaatcctg aacagaatgt
     1321 tactcctctg agtattttct gttaagaaaa tatacactta gcacagttac aataaatcct
     1381 accccctgta agaatgtgaa ttgttcatcc aaaaacaacc atgacaaaaa taatgcaact
     1441 agcggaataa agtacaacat tatccctgcc aaatgaactg ggagccaacg caaggagttc
     1501 aagtaaaaac aaaaagctaa aaaatattgt aatattccag atgaaaaaac aataatcacg
     1561 gattccaacg gaagataaat tgatgattta gatataaaaa taaagagcga tgacagtata
     1621 agggagaatg tcaactgtcc gctcaataat gtgataggct caaacgattt aataaggcga
     1681 gacgatataa caacataaaa tgctgccgat aacacaccgg caacaacaag acaatatcca
     1741 acaatattat tcgatccatt actgatgtct ggcaaggcta ccaaaatact gccaacaatt
     1801 gcacctataa ggaacaatat aaaatattgc ggggaattaa ttttaactga gcaaataaga
     1861 acagacaaca ccaatataaa cactgattca agtgaaaaaa taattgatgc gcttcctgct
     1921 gaaataaaat aaagtccgta gagtgtaaaa gtatacgcta agaatggttc aaaaacgcct
     1981 gtcgcataag caagtatcgc ttttgagttt aatgggagtt tttttctttt tataaaaaga
     2041 actatccaag atagtattac tgcactacaa atctgccaga aaaacacccc tccggcatct
     2101 agttcttcaa ctcctttttt gctcattacg atagctgccc cccatgagaa cgctgctaaa
     2161 aaagcaaaaa gcattccttt aatcatatta atcatcctct ttctcataaa ggggtttgtt
     2221 ttcaaatttc cttggttgaa aggagttaaa aaacatagat gcatcatcta caggaatacc
     2281 aataaactct ccataataag gatcatctat aggaaactct tctaatgaaa cataaaacaa
     2341 tacattccag ttgaagatca ttggatcact attttctatt tcatggagca atctttcatc
     2401 cttagttaat tctcctggaa ttaatacatc agtatgataa aaaccgctgt aataagaact
     2461 attaccggtg tgcactgggc atccaaaacg atccaaatta gattctgaat gccatgttgt
     2521 agaaatccct tccggatgtg aatacccacc cttaccaaca gactgaatag tcatgttacg
     2581 aatatccgct aacgcttgtt cttgatcttt atagaaacct ttttctatcg ccagcctcat
     2641 aaaatgcccc ggggcattta cagaaataag tattccccct ggtattcttc tatcatgatt
     2701 tcttgttcta tgagcagaag agtaaaaaac attaacacca gccttatata tttttagccc
     2761 atctttatcc tgaaatggta cgctttcagt ataaataaca tcctctttta ttggatagca
     2821 ctctggcata tgcagcgaac aaatatattt ttgtatgtcc actaactctt ctgatggacg
     2881 agcaaaggca agttgtggat gaataaaata aatgagatgc gcactgacct ctcctcttct
     2941 tgcgcgttct ttaaaacgaa ctctttcatt acgcaaaaaa tcaaacaaat gaccatcatc
     3001 attatatagt tgggggctat ttacaataga taaatggaaa tcaagccctt taattttctt
     3061 gcttgccaat ttaccaaata cacagggctg attgcctgac acccattttc ttagtaaatc
     3121 ttcaatttta tctttagaag tttcgttaaa gataaatgaa tgaatattat caatatcttt
     3181 tccaaatgaa aaactggatg ataattgtgg tagtttattt atacgttgtt gaagattcat
     3241 gaaagctccc acaagacacc tcatatattt ttttatatac tgaaactaca ttatatttat
     3301 taccggcgta aaacgaaata atttattatc gttaccgata ttttaaaaaa atcattattt
     3361 gcacagtgtt cgagttgtta gtatcactcc ttcctgaaaa tccgctccat ttaccataac
     3421 gtcgcattgt acgcaccgcc aaaacgcgtt cggtgcgatc acggcagcag acaggtaaaa
     3481 atggcaacaa accacccgaa aaactgccgc gatcgcacct gataaatttt aaccgcatga
     3541 atacctatgc aaccagatgc tacaggccac attagcccgc cttaatccac tgaacacgtc
     3601 atttttcatg gtttcaccat cccagcgaag ggccatccag tgtccgctcc tggatttccg
     3661 gctgacgctc ccgctccaga gataactcat gttcgcgttc ctgcatcagc cgttcatccc
     3721 ttatctcctg ttctcgctgt ataactggct caagcgttct gtccgctcgc tcaagtgctg
     3781 cacctgctga ctcaactgca tgactcgccc gttcagcatc gcgttgtccc gttgcgtaag
     3841 cgaaaacatt ttctgcaatt ccacgaaggc gttctcccat tcgttcagcc gctgcatata
     3901 gtcctgttgc agttgctcta atgcgttcag caaatgtctt tccagctccg tcatgctctg
     3961 tcactcctgc accagtctca ctgcgttcag tttgccgttg tccttcgtcc agttcgtttc
     4021 ggctttcatc cccttcggca acaccagaaa acgtccgttg ctgtcctcgt gataacgcac
     4081 gccccatgtc ttcgcgttca gcttctccag actctctttc tgctcgcgga gaatattcat
     4141 attcgcgttt atcttcatgc cctggtacca cagcagactc ccggtcgtgg caaacatcag
     4201 tactgagacg ataatcagcc acagccagcg tttcacgctc attttcagta cggttttcca
     4261 gtgcgcgtcc atcgtatcga cggtcgtttt ctgatacctc tccagcagtt ctttcagggc
     4321 tgttgtatgg tcgttgatag cgttcctgat taaagattcg tttgaggtca gttccctgtt
     4381 tacagattct tcgagcttcc tgaactcgtc gttcagcatt ttctctgtag attcggctct
     4441 ctctttcagc tttttctcga actccgcgcc cgtctgtaaa agattgctca taaaacgctc
     4501 ctttcagtct gatattcctc ccgccgttcg ggtctgcaat gctgatactg cttcgcgtca
     4561 ccctgaccac ttcaagcccc gcctctgtga gcgcctgaat cacatcctga cggcctttta
     4621 tctctccggc atggtaaagc gcgtctatcc cgcgtgtgac gccctcagca agcgcctgtt
     4681 tcgtttccgg caggttatca ggaagggtca gcgtccggcg gttctccggg gcgttggggt
     4741 catgcagacc gtaatggtga ttcaccagcg tctgccaggc atcaattctc ggcctgtctg
     4801 cccggtcgta gtacggctgg aggcgttttc cggtctgtag ctccatgttc ggaatgacaa
     4861 aattcagctc aagccgtccc ttgtcctggt gctccaccca caggatgctg tactgatttt
     4921 tctcgagacc gggcatcagt acacgctcaa agctcgccat cactttttca cgccctccag
     4981 gcggcagctc cttctccgcg aacgacagaa cacctgacgt gtatttcttc gcaaatggcg
     5041 tggcatcgat gagttcccgg acctcttccg gattcccctg aagcaccgtt gccccttccc
     5101 ggttacgctc ccttcccagc aggtaatcaa ccggaccact gccaccacct tttcccctgg
     5161 catgaaactt aactatcatc ccgcgccccc tgttccctga ccgccagacg cagccggcgc
     5221 agctcatccc cgatgatcat cagtgcggcc accacctgaa cccggtcacc ggaagaccac
     5281 tgcccgctgt tcaccttcct cgctgtctgg ttaaggttat tcccgatggc ggccagctga
     5341 cgcagtaacg gcggtgccag tgtcggcagc ttcccggaac gggcaaccgg ctcacccagg
     5401 cagacccgcc gcatccatac cgccagttgt ttaccctcac agcgttccag taaccgggca
     5461 tgttcatcat cagtaacccg tatcgtgagc atcctctcgc gttt
//
