LOCUS       NZ_CP070095             5570 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1370 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP070095
VERSION     NZ_CP070095.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357512
            Assembly: GCF_016904335.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5570)
  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  JOURNAL   Unpublished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 5570)
  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                   :: 1046.79x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:28:47
            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)                     :: 5,174
            CDSs (total)                      :: 5,056
            Genes (coding)                    :: 4,837
            CDSs (with protein)               :: 4,837
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 78 of 219
            Pseudo Genes (incomplete)         :: 148 of 219
            Pseudo Genes (internal stop)      :: 41 of 219
            Pseudo Genes (multiple problems)  :: 45 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070095.1.
            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..5570
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1370"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1370"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(join(5194..5570,1..580))
                     /locus_tag="I6L00_RS00005"
                     /old_locus_tag="I6L00_00005"
     CDS             complement(join(5194..5570,1..580))
                     /locus_tag="I6L00_RS00005"
                     /old_locus_tag="I6L00_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /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_223673566.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVYKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            651..1790
                     /gene="dcm"
                     /locus_tag="I6L00_RS00010"
                     /old_locus_tag="I6L00_00010"
     CDS             651..1790
                     /gene="dcm"
                     /locus_tag="I6L00_RS00010"
                     /old_locus_tag="I6L00_00010"
                     /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_033550328.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAIMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            complement(2157..2390)
                     /locus_tag="I6L00_RS00015"
                     /old_locus_tag="I6L00_00015"
     CDS             complement(2157..2390)
                     /locus_tag="I6L00_RS00015"
                     /old_locus_tag="I6L00_00015"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2397..2915)
                     /locus_tag="I6L00_RS00020"
                     /old_locus_tag="I6L00_00020"
     CDS             complement(2397..2915)
                     /locus_tag="I6L00_RS00020"
                     /old_locus_tag="I6L00_00020"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2953..3384)
                     /locus_tag="I6L00_RS25750"
                     /pseudo=""
     CDS             complement(<2953..3384)
                     /locus_tag="I6L00_RS25750"
                     /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(3593..3916)
                     /locus_tag="I6L00_RS00030"
                     /old_locus_tag="I6L00_00030"
     CDS             complement(3593..3916)
                     /locus_tag="I6L00_RS00030"
                     /old_locus_tag="I6L00_00030"
                     /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            3980..4171
                     /locus_tag="I6L00_RS00035"
                     /old_locus_tag="I6L00_00035"
     CDS             3980..4171
                     /locus_tag="I6L00_RS00035"
                     /old_locus_tag="I6L00_00035"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4257..4344)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          4368..4913
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.171"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2054..3603)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.374"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cggaaatcaa cattgtattt cttttgttag atgtgtactg gactacacct ggcataacaa
       61 gatctacaag tttacctatt tggttttttt gaaaaaatga cttcccaata gccccctgca
      121 catcaacagg aattcctgcc cccatcatta atagctcaag aatagactca aactcttttc
      181 ctgccctgct acgtctggat tgagtgttag acagtgccaa atcatatatg tgtgtagggt
      241 attccatcgt aaaatcacga atggcatcat aaggactcat atcttttatt ctttcttcat
      301 caataagata tgataacatt cttgttgtga attctttttc aaatggttca aattctttcc
      361 aacagttttt tctcattgca attatatatt cacttggatt attcaaaaaa taatcactat
      421 ttttttgatc ataccctaaa tcacaaaatg ttttataaac caaagcaaat ggcgtaataa
      481 aatgcgactt tctctcttta gaaattagag ttttaaattc accaggactc aatctttgca
      541 taaaaaataa ccttttatat ctacttgaaa gttttttcat gcacgttcat aattggaatc
      601 aaaacaggac aaattgtcct aaaaccaaca cttaattctg gtagacatgc atgactgata
      661 atatcgcagc aacaatcaaa ggaaaaagag aaagacttca tatgactcaa aaagagtttg
      721 cagacgccct tggtctttca aaatatggag acagaaccat aagaagatgg gagcgcgggg
      781 aaacaaaacc tactggggcg gaactaaaag caattatgga ctttccagac acaccacctt
      841 acccaaacaa cgagaatggc agatatcgca tgatcgattt atttgctgga atcggtggaa
      901 ccagacttgg atttcatcaa actaacgctg taaatgttgt tttttccagc gaatgggata
      961 agtttgctca aaagacatat catgcaaatt atggtgattt ccctgatggg gacataacaa
     1021 aaatcgatga aaaagatatt cctgatcatg aaattcttgt cggtgggttt ccttgcgtag
     1081 cattctctca agcagggctc aaaaaaggat ttaatgatac aagaggaact ttgttttttg
     1141 atatagcaag gataataaag gaaaaaaaac ctcatgcttt tttacttgaa aatgtaaaaa
     1201 acttgctagg acatgataaa ggtagaactt tttcaataat aaaaaacaca cttgaagaat
     1261 tgaattacac tgtgtattac aatatcttcg ctgcaaaaga ctttggtgtt ccacaaaata
     1321 gagaacgcat atacattgta ggctttaata aagaaaaagt aagaaatcat gaacatttta
     1381 cttttccaac cccgttaaaa acaaaaacaa gagttggaga tattcttgaa aagagcgtag
     1441 acaataaata tacgctatca gatgcgctct ggaatggaca ccaacgcagg aaacttgtaa
     1501 atgcagcagc cggtaaaggc tttgggtatg gtttatttaa tgaaaatagc ccatatacta
     1561 ataccataag tgcgaggtac tataaagatg gtagtgaaat attaatagag caaaaaggaa
     1621 gtaacccaag aaaaataact ccgcgggaag cgtcaagact tcaagggttt cctagtgatt
     1681 ttattatccc tgtatcggat acacaggctt ataagcaatt tgggaattca gtcgcagtcc
     1741 ctgttatcaa tgcaatagca gaaaaaatca tatcgacctt agattcataa actaagtcat
     1801 aaggacacaa tgcggcccag aatccaatta ccccccccat atggatttac cataacgtcg
     1861 cattacgcgc accgctgaaa cgcgttcagc gcgatcacgg cagcagacag gtaaaaatgg
     1921 caacaaacca cccgaaaaac tgccgcgatc gcgcctgata aattttaacc gcatgaatac
     1981 ctatgcaacc agatggtaca ggccacatta acccctctta atccactgaa gctgccattt
     2041 ttcatggttt caccatccca gcgaaggacc atccagcgtg cgttcctgta tttccggctg
     2101 acgctcccgt tccagggata acgcatgttc gcgctcctgt atcagccgtt cctctcttat
     2161 ctccagttct cgctgtataa ctggctcaag cgttctgtct gctcgctcaa gtgctgcacc
     2221 tgctgactca actgcatgac ccgctcgttc agcatcgcgt tgtcccgttg cgtaagcgaa
     2281 aacatcttct gcaattccac gaaggcgctc tcccattcgc tcagccgctg catatagtcc
     2341 tgttgcagct gctctaaggc gttcagcaaa tgtatttcca gctctgtcac tctgtgtcac
     2401 tccttcagat gtacccactc tttcccctga aagggaatca cctccgctga tttcccgtac
     2461 ggaaggacaa ggaatttcct gttcccgtcc tgcacaaact ccacgcccca tgtcttcgcg
     2521 ttcagtttct gcaatgtctc ttcctgcttc ctgatttctt ccaggttcgt ctgtatccgt
     2581 ccgccaagat accagagcgt cccgccactc gcggtaaaca ggagaaagac tatccccagt
     2641 aacatcatgc ccgtattccc tgccagcttt aacacgtcct tcctgtgctg catcatcgcc
     2701 tctttcaccc cttcccggtg tttttccagc gatttctctg tcgaggctgt gaacagggct
     2761 atagcgtctc tgattttcgt ctcgtttgag gtcacagcct cgctgacaga ctcgccgagc
     2821 ttcctgaact cgtcgttcag cattttctct gtagattcgg ctctctcttt cagctttttc
     2881 tcgaactccg cgcccgtctg taaaagattg ctcataaaac gctcctttca gtctgatatt
     2941 cctcccgccg ttcgggtctg caatgctgat actgcttcgc gtcaccctga ccacttcaag
     3001 ccccgcctct gtgagcgcct gaatcacatc ctgacggcct tttatctctc cggcatggta
     3061 aagtgcgtct ataccgcgtg taacgctctc agcaagtgcc tgtttcgttt ccggcaggtt
     3121 atcaggaaga gtcagcgtcc ggcggttctc cggggcgttg gggtcatgca gtccgtaatg
     3181 gtgattcacc agcgtctgcc aggcatcaat tctcggcctg tctgcgcggt cgtagtacgg
     3241 ctggagacgt tttccggtct gtagctccat gttcggaatg acaaaattca gctcaagccg
     3301 tcccttgtcc tggtgctcca cccacagaat gctgtactga tttttttcga gaccgggcat
     3361 cagtacacgc tcaaagctcg ccatcacttt ttcacgtcct cccggcggca gctccttctc
     3421 cgcgaacgac agaacaccgg acgtgtattt cttcgcaaat ggcgtggcat cgatgagttc
     3481 ccggacttct tccggattac cctgaagcac cgttgcgcct tcgcggttac gctccctccc
     3541 cagcaggtaa tcaaccggac cactgccacc accttttccc ctggcatgaa atttaactat
     3601 catcccgcgc cccctgttcc ctgacggcca gacgcagccg gcgcagctca tccccgatgg
     3661 ccatcagtgc ggccaccacc tgaacccggt caccggaaga ccactgcccg ctgttcacct
     3721 tacgggctgt ctgattcagg ttatttccga tggcggccag ctgacgcagt aacggcggtg
     3781 ccagtgtcgg cagtttcccg gaacgggcaa ccggctcccc caggcagacc cgccgcatcc
     3841 ataccgccag ttgtttaccc tcacagcgtt caagtaacct ggcatgttca tcatcagtaa
     3901 cccgtatcgt gagcatcctc tcgcgtttca tcggtattat taccccatga acagaaatcc
     3961 cccttacacg gaggcatcag tgactaaaca ggaaaaaaca gcccttaaca tggcgcgctt
     4021 tatcagaagc cagacattaa cgctgctgga aaagctcaac gaactggacg cggatgaaca
     4081 ggcagacatc tgtgaatcgc ttcacgacca cgccgatgag ctttaccgca gctgcctcgc
     4141 acgtttcggg gatgacggtg aaaacctctg acacatgcag ctcccagaga cggtcacagc
     4201 ttgtctgtga gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag caggttttag
     4261 cgggtgtcgg ggcgcagccc tgacccagtc acgtagcgat agcggagtgt atactggctt
     4321 aactatgcgg catcagtgcg gattgtatga aaagcacgcc atgccgggtg tgaaatgccg
     4381 cacagatgcg taaggagaac ataccgcatc aggcgctctt ccgcttcctc gctcactgac
     4441 tcgctgcgct cggtcgttcg gctgcggcaa gcggtgccgg ctcactcaaa ggcggaaata
     4501 cggttatcca cagaatcagg ggataaggcc ggaaagaaca tgtgagtaaa aaggcaaagg
     4561 gcaacaaaag gccgccccgc tggcgttttt ccataggctc cgcccccctg acgagcatca
     4621 caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggactataaa gataccaggc
     4681 gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata
     4741 cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac gctgttggta
     4801 tctcggcccg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca
     4861 gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccag taagacacgc
     4921 cttaacgcca ctggcagcag ccactggtaa ccggattagc agagcgagat ttatccagat
     4981 gcttacagag ttcttgaagt gatggcctaa ctacggctac actggaagga cagtatttgg
     5041 tatctgtgct ctgctgaagc cagattacct cggttagata atctgccagg attagctaac
     5101 cttcgaaaaa accacctgcc agggtggttt tttcgtttac aggtccaaga ttacgcgcag
     5161 aaaaaaagga tctcaagaga tccttttagt tttttagtca aaaagagcac taagcctatt
     5221 tctataataa ttaacaacat aagggaaatc actatatttt tctatttgtt ttaatattga
     5281 ctgttgaatt tcctcttttt cagagtctgt gtaacttaca ttattccact ttcttgataa
     5341 ttccattgct gactgtagca tatcttcaaa ggttagcacc ctattattat ttttatattt
     5401 gaaattttta ttttctatcg tcgttacaac gaccacatta gcctcgtaca atatatttat
     5461 tgtctcctcg ctaaaagaat catctagtgt agctagatac atttctctaa ttcctgttct
     5521 attaacctct tcaggtactt cttgccatcg ctccctcagc gttgttttag
//
