LOCUS       NZ_CP070128             5171 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1292 plasmid unnamed4.
ACCESSION   NZ_CP070128
VERSION     NZ_CP070128.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357434
            Assembly: GCF_016904475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5171)
  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  JOURNAL   Unpublished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 5171)
  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                   :: 1353.32x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:30:25
            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)                     :: 5,003
            CDSs (total)                      :: 4,888
            Genes (coding)                    :: 4,705
            CDSs (with protein)               :: 4,705
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 71 of 183
            Pseudo Genes (incomplete)         :: 119 of 183
            Pseudo Genes (internal stop)      :: 40 of 183
            Pseudo Genes (multiple problems)  :: 44 of 183
            Pseudo Genes (short protein)      :: 4 of 183
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070128.1.
            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..5171
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1292"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1292"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(409..1548)
                     /gene="dcm"
                     /locus_tag="I6K22_RS24665"
                     /old_locus_tag="I6K22_24665"
     CDS             complement(409..1548)
                     /gene="dcm"
                     /locus_tag="I6K22_RS24665"
                     /old_locus_tag="I6K22_24665"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="WP_201478808.1"
                     /translation="MTDNIAAIIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVIDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            1658..2575
                     /locus_tag="I6K22_RS24670"
                     /old_locus_tag="I6K22_24670"
     CDS             1658..2575
                     /locus_tag="I6K22_RS24670"
                     /old_locus_tag="I6K22_24670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001189381.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_001189380.1"
                     /translation="MQRLSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYF
                     LNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTH
                     IYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVM
                     PGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILY
                     EANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILK
                     QIEKYSDFPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            complement(2759..2929)
                     /locus_tag="I6K22_RS25100"
     CDS             complement(2759..2929)
                     /locus_tag="I6K22_RS25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_059287940.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGNRIRRALMC
                     NQYYRVLEVMA"
                     /name="hypothetical protein"
     gene            complement(3600..3791)
                     /locus_tag="I6K22_RS24675"
                     /old_locus_tag="I6K22_24675"
     CDS             complement(3600..3791)
                     /locus_tag="I6K22_RS24675"
                     /old_locus_tag="I6K22_24675"
                     /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_042634456.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENH"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3858..4181
                     /locus_tag="I6K22_RS24680"
                     /old_locus_tag="I6K22_24680"
     CDS             3858..4181
                     /locus_tag="I6K22_RS24680"
                     /old_locus_tag="I6K22_24680"
                     /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_204678132.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGNLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4390..>4821
                     /locus_tag="I6K22_RS25105"
                     /pseudo=""
     CDS             4390..>4821
                     /locus_tag="I6K22_RS25105"
                     /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            4859..>5171
                     /locus_tag="I6K22_RS25110"
     CDS             4859..>5171
                     /locus_tag="I6K22_RS25110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_251301828.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHQEGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     "
                     /name="MbeB family mobilization protein"
     Typing          3428..3515
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          complement(2858..3402)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.881"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4172..4581
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="4.5000000000000005e-87"
ORIGIN
        1 agacagaacg cttgagccag ttatacagcg agaactggag ataagagagg aacggctgat
       61 acaggagcgc gaacatgcgt tatccctgga acgggagcgc cagctggaaa tacaggaacg
      121 cacactggat ggtccttcgc tgggatggtg aaactatgaa aaatggcagg ttaagtggat
      181 taagacgggc taatgtggtc tgtaccatct ggttgcatag gtattcatgc ggttaaaatt
      241 tatcaggcgc gatcgtggca gtttttcggg tggtttgttg ctatttttac ctgtctgctg
      301 ccgtgatcgc gctgaacgcg ttttagcggt acgtacaatg cgacgttatg gtaaatccat
      361 atggggggta attggattct gggccgcatt gtgtccttat gacttagttt atgaatctaa
      421 ggtcgatatg attttttctg ctattgcatt gataacaggg actgcgactg aattcccaaa
      481 ttgcttataa gcctgtgtat ccgatacagg gataataaaa tcactaggaa acccttgaag
      541 tcttgacgct tcccgcggag ttatttttct tgggttactt cctttttgct ctattaatat
      601 ttcgctacca tctttatagt acctcgcact tatggtatta gtatatgggc tattttcatt
      661 aaataaacca tacccaaagc ctttaccggc tgctgcattt acaagtttcc tgcgttggtg
      721 tccattccag agcgcatctg atagcgtata tttattgtct acgctctttt caagaatatc
      781 tccaactctt gtttttgttt ttaatggggt tggaaaagta aaatgttcat gatttcttac
      841 tttttcttta ttaaagccta caatgtatat gcgttctcta ttttgtggaa caccaaagtc
      901 ttttgcagcg aagatattgt aatacacagt gtaattcaat tcttcaagtg tgttttttat
      961 tattgaaaaa gttctacctt tatcatgtcc tagcaagttt tttacatttt caagtaaaaa
     1021 agcatgaggt tttttttcct ttattatcct tgctatatca aaaaacaaag ttcctcttgt
     1081 atcattaaat ccttttttga gccctgcttg agagaatgct acgcaaggaa acccaccgac
     1141 aagaatttca tgatcaggaa tatctttttc atcgattttt gttatgtccc catcagggaa
     1201 atcaccataa tttgcatgat atgtcttttg agcaaactta tcccattcgc tggaaaaaac
     1261 aacatttaca gcgttagttt gatgaaatcc aagtctggtt ccaccgattc cagcaaataa
     1321 atcgatcatg cgatatctgc cattctcgtt gtttgggtaa ggtggtgtgt ctggaaagtc
     1381 tataactgct tttagttccg ccccagtagg ttttgtttcc ccgcgctccc atcttcttat
     1441 ggttctgtct ccatattttg aaagaccaag ggcgtctgca aactcttttt gagtcatatg
     1501 aagtctttct ctttttcctt tgattattgc tgcgatatta tcagtcatgc atgtctacca
     1561 gaattaagtg ttggttttag gacagtttgt cctgttttga ttccaattat gaacgtgcat
     1621 gaaaaaactt tcaagtagat ataaaaggtt attttttatg caaagattaa gtcctggtga
     1681 atttaaaact ctaatttcta aagagagaaa gtcgcatttt attacgccat ttgctttggt
     1741 ttataaaaca ttttgtgatt tagggtatga tcaaaaaaat agtgattatt ttttgaataa
     1801 tccaagtgaa tatataattg caatgagaaa aaactgttgg aaagaatttg aaccatttga
     1861 aaaagaattc acaacaagaa tgttatcata tcttattgat gaagaaagaa taaaagatat
     1921 gagtccttat gatgccattc gtgattttac gatggaatac cctacacaca tatatgattt
     1981 ggcactgtct aacactcaat ccagacgtag cagggcagga aaagagtttg agtctattct
     2041 tgagctatta atgatggggg caggaattcc tgttgatgtg cagggggcta ttgggaagtc
     2101 attttttcaa aaaaaccaaa taggtaaact tgtagatctt gttatgccag gtgtagtcca
     2161 gtacacatct aacaaaagaa atacaatgtt gatttccgct aaaacaacac tgagggagcg
     2221 atggcaagaa gtacctgaag aggttaatag aacaggaatt agagaaatgt atctagctac
     2281 actagatgat tcttttagcg aggagacaat aaatatattg tacgaggcta atgtggtcgt
     2341 tgtaacgacg atagaaaata aaaatttcaa atataaaaat aataataggg tgctaacctt
     2401 tgaagatatg ctacagtcag caatggaatt atcaagaaag tggaataatg taagttacac
     2461 agactctgaa aaagaggaaa ttcaacagtc aatattaaaa caaatagaaa aatatagtga
     2521 tttcccttat gttgttaatt attatagaaa taggcttagt gctctttttg actaaaaaac
     2581 taaaaggatc tcttgagatc ctttttttct gcgcgtaatc ttggacctgt aaacgaaaaa
     2641 accaccctgg caggtggttt tttcgaaggt tagctaatcc tggcagatta tctaaccgag
     2701 gtaatctggc ttcagcagag cacagatacc aaatactgtc cttccagtgt agccgtagtt
     2761 aggccatcac ttcaagaact ctgtagtact gattacacat caatgctctg cgaatccggt
     2821 taccagtggc tgctgccagt ggcgttaagt cgtgtcttac cgggttggac tcaagacgat
     2881 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     2941 tggagcgaac gacctacacc gggccgagat acctacagcg tgagctatga gaaagcgcca
     3001 cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag
     3061 agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc
     3121 gccacctctg acttgagcgt cggtttttgt gatgctcgtc agggggggcg gagcctatgg
     3181 aaaaacgcca gcggcgcggc ctttcgttgg gctttgcctt tttgctcaca tgttctttcc
     3241 ggccttatcc cctgattctg tggataaccg tattaccgct tttgagtgcg ccggtaccgc
     3301 tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagtgtcg
     3361 gaagttgcat tttctcctta cgcatctgtg cggcatttca catcggctat ggtgcacttt
     3421 tcatacaatc cgcactgatg ccgcatagtt aagccagtat acactccgct atcgctacgt
     3481 gactgggtca gggctgcgcc ccgacacccg ctaaaatctg ctgacgcgcc ctgacgggct
     3541 tgtctgctcc cggcatccat tcacagacaa gttgtgtacg tctccgggag ctgcatgtgt
     3601 cagtggtttt caccgtcatc cccgaagcgt gcgaggcagc tgcggtaaag ctcgtcggcg
     3661 tggtcgtgaa gcgattcaca gatgtctgcc tgttcatctg cgtccagttc gttgagcttt
     3721 tccagcagcg ttaatgtctg gcttctgata aagcgggcca tgttaagggc ggttttttcc
     3781 tgtttagtca ctgatgcctc cgtgtaaggg ggggatttct gttcatgggg gtaatgatac
     3841 cgatgaaacg cgagaggata ctcacgatac gggttactga tgatgaacat gcccggttac
     3901 tggaacgctg tgagggtaaa cagctggcgg tatggatgcg gcgggtctgt ctgggtgagc
     3961 cggttgcccg ctccgggaat ctgccgacac tggcaccgcc gttactgcgt cagctggccg
     4021 ccatcgggaa taacctgaat cagactgcga ggaaggtgaa cagcgggcag tggtcttccg
     4081 gtgaccgggt tcaggtggtg gccgcactga tggccatcga gagagagttg cgcagcttac
     4141 ggcaggtggt cagggaacag ggagtgcggg atgatagtta agtttcatgc caggggaaaa
     4201 ggtggtggca gtggtccggt tgattacctg ctgggaaggg agcgtaaccg ggaaggggca
     4261 acggtgcttc aggggaatcc ggaagaggtc cgggaactca tcgatgccac gccatttgcg
     4321 aagaaataca cgtcaggtgt tctgtcgttc gcggagaagg agctgccgcc gggaggacgt
     4381 gaaaaagtga tggcgagctt tgagcgtgta ctgatgcccg gtctcgaaaa aaatcagtac
     4441 agcatcctgt gggtggagca ccaggacaag ggacggcttg agctgaattt tgtcattccg
     4501 aacatggagc tacagagcgg aaaacgcctc cagccgtact acgaccgggc agacaggccg
     4561 agaattgatg cctggcagac gctggtgaat caccattacg gtctgcatga ccccaacgcc
     4621 ccggagaacc gccggacgct gacccttcct gataacctgc cggaaacgaa acaggcgctt
     4681 gcagagagcg tcacacgcgg gatagacgct ctttatcatg tcggggagat aaaaggccgt
     4741 caggatgtga ttcaggcgct cacggaggcg gggcttgaag tggtcagggt gacgcgaagc
     4801 agtatcagca ttgcagaccc gaacggcggg aagaatatca ggctgaaagg agcgttttat
     4861 gagcaatctt ttacagacgg gcgcggagtt cgagaaaaag ctgaaagaga gagccgaatc
     4921 tacagagaaa atgctgaacg acgagttcag gaagctcggc gagtctgtca gcgaggctgt
     4981 gacctcaaac gagacgaaaa tcagagacgc tatagccctg ttcacagcct cgacagagaa
     5041 atcgctggaa aaacaccagg aaggggtgaa agaggcgatg atgcaacaca ggaaggacgt
     5101 gttaaagctg gcagggaata cgggcatgat gttactgggg atagtctttc tcctgtttac
     5161 cgcgagtggc g
//
