LOCUS       NZ_CP023904             4011 bp    DNA     circular CON 14-JUN-2024
DEFINITION  Escherichia coli strain FDAARGOS_433 plasmid unnamed8, complete
            sequence.
ACCESSION   NZ_CP023904
VERSION     NZ_CP023904.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07312477
            Assembly: GCF_002589795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4011)
  AUTHORS   Croxen,M., Tallon,L., Sadzewicz,L., Ott,S., Zhao,X., Nagaraj,S.,
            Vavikolanu,K., Aluvathingal,J., Nadendla,S., Geyer,C. 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  JOURNAL   Unpublished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 4011)
  AUTHORS   Croxen,M., Tallon,L., Sadzewicz,L., Ott,S., Zhao,X., Nagaraj,S.,
            Vavikolanu,K., Aluvathingal,J., Nadendla,S., Geyer,C. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-OCT-2017) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0
            Genome Coverage                   :: 696.335x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002589795.1-RS_2024_06_14
            Annotation Date                   :: 06/14/2024 04:40:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,097
            CDSs (total)                      :: 4,972
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 279
            CDSs (without protein)            :: 279
            Pseudo Genes (ambiguous residues) :: 0 of 279
            Pseudo Genes (frameshifted)       :: 87 of 279
            Pseudo Genes (incomplete)         :: 190 of 279
            Pseudo Genes (internal stop)      :: 46 of 279
            Pseudo Genes (multiple problems)  :: 39 of 279
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023904.1.
            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..4011
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_433"
                     /isolation_source="Rectal"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_433"
                     /db_xref="taxon:562"
                     /plasmid="unnamed8"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2015-12"
                     /collected_by="BC Centre for Disease Control"
     gene            join(3966..4011,1..173)
                     /locus_tag="CRN16_RS27575"
     CDS             join(3966..4011,1..173)
                     /locus_tag="CRN16_RS27575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041626.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFEAESGTRQDAERYTCA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            620..733
                     /locus_tag="CRN16_RS28515"
     CDS             620..733
                     /locus_tag="CRN16_RS28515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_194505760.1"
                     /translation="MHEPPVQPDRCVLSGNYRLESNPERHDLTPLAAAIGN"
                     /name="replication initiation protein"
     gene            complement(897..1679)
                     /locus_tag="CRN16_RS26770"
                     /old_locus_tag="CRN16_26765"
     CDS             complement(897..1679)
                     /locus_tag="CRN16_RS26770"
                     /old_locus_tag="CRN16_26765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000140057.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_225877509.1"
                     /translation="MTERILFVFEGEKTEKTITDSLLKKFIENDKRVVLSSFKTDIYSL
                     YKLMSEDEDLDVFAVLKEKNPDLVDFDRDSFSQLFLFFDYDGHAPTASDEKIDRLLSFF
                     NEETENGKLFISYPMVESIKCISHIDAIEDFCRHTVKICDCSKFKGYVAEYAHKSLIHF
                     NLYSDEAWNDVVRMHCVKSNFIMKGNMIFPSNYFSQKDIFSMQKSKYIDPNGSVSTLSS
                     FPMLLLDFFGHQRLFVLVSGEQIEDGDVLSSEEAQRTI"
                     /name="hypothetical protein"
     gene            complement(1672..2796)
                     /locus_tag="CRN16_RS26775"
                     /old_locus_tag="CRN16_26770"
     CDS             complement(1672..2796)
                     /locus_tag="CRN16_RS26775"
                     /old_locus_tag="CRN16_26770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000640319.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_097514844.1"
                     /translation="MIYRFEVEGFKGFSDKLVFDLTHRKNYEFNQDCILDGVVKKSLVY
                     GKNGIGKSNLGLALFDIVAHLTEFNVNDGMYNNYINALNNSGIARFKYDFKFGDNIVTY
                     LYGKRSVKELVFEELFINGRLVTKFNRVLDSNAYFSLSGTETLNTALAESKISIINYIK
                     NNAILNDGIEKDLFNQFIVFVEKMLYFRSLDSNNYLGLEMGRHLITPDIVERGNVDDFE
                     RFLNKAGVKCKLCVMKIQSNNGVVEDIGFDFGSKQIPFYGVASTGTKSLALFYYWLQRF
                     KDEKCVSFIFVDEFDAFYHHSLSMLIVKEMKKAGAQVIITTHNTNVMTNELLRPDCYFI
                     MDDKGITPLFEKTDKELREAHNIEKMYKAGTFND"
                     /name="ATP-binding protein"
     gene            complement(3371..3694)
                     /gene="mobA"
                     /locus_tag="CRN16_RS26785"
                     /old_locus_tag="CRN16_26780"
     CDS             complement(3371..3694)
                     /gene="mobA"
                     /locus_tag="CRN16_RS26785"
                     /old_locus_tag="CRN16_26780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          complement(3704..3929)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.75"
                     /coverage="99.0"
                     /evalue="2.28e-73"
     Typing          168..689
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.156"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(3375..3694)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="4.33e-63"
ORIGIN
        1 aaagccagag cctgacgctg ctcgaaaaac tggactcact cgatgctgat gcacaggccg
       61 ccatgtgtga gaaactgcac gaactcgcag aagaactcca gaacagcata cagacacgct
      121 ttgaagcgga aagtggcacc agacaggatg cagaacggta tacctgtgcg taaggagaaa
      181 atgacacata aggctctctt ccgcttcctc gctcactgac tcgctacgct cggccgttcg
      241 gctgcggcga gcggtatcag ctcactcaaa aacggtaatg cggtgatcca cagaatcagg
      301 ggataaagcc aaaaggagca tgtgagcaaa aaacgagaac caggaaaagg ccgcgcctat
      361 ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac gctcaagtca
      421 gaggtggcga aacccgacag gactataaag ataccaggcg tttccccccg gaagctccct
      481 cgtgcgctct cctgttccga ccctgccgtt taccggatac ctgtccgcct ttctcccttc
      541 gggaaacgtg gcgctttctc atagctcacg ctgttggtat ctcggcccgg tgtaggtcgt
      601 tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct gcgtcttatc
      661 cggtaactat cgtcttgagt ccaacccgga aagacacgac ttaacgccac tggcagcagc
      721 cattggtaac tgatttagag gagttagtct tgatgttatg cgccggttaa ggctaaactg
      781 aaagaacaag ttttggtgac tgagctcctc tattctatta gccagttacc tcggttcaga
      841 aacttgccgg ttactgaacc ttcgaaaaaa ccaccttgcc gggtggtttt ttcttttcaa
      901 atagtacgct gggcttcctc cgaactcaat acgtctccat cctcaatttg ttcaccgctg
      961 accagcacaa acaatctttg gtgcccaaaa aagtctaaaa gtaacatcgg gaatgaactt
     1021 aatgtagata cagagccatt tggatctata tattttgatt tctgcatact gaatatatct
     1081 ttctgtgaaa aataattaga aggaaaaatc atattcccct tcattatgaa attagatttc
     1141 acacaatgca tcctaaccac atcattccaa gcctcatcag aatacaaatt aaagtgaatc
     1201 aatgacttat gagcatattc tgcaacatac cccttaaact tagaacaatc acatattttt
     1261 actgtatgcc tacaaaaatc ctcaatcgca tcaatatgcg agatacattt tatagactca
     1321 accataggat aactgataaa taatttaccg ttttcagttt cctcattaaa aaaacttagt
     1381 agcctgtcta tcttttcatc agaagcagtt ggagcatgcc cgtcataatc aaagaacaga
     1441 aaaagctgag agaaagaatc tctatcaaaa tctactaagt caggattttt ttccttcaac
     1501 acggcaaata catcaagatc ttcatcctca ctcatcaact tataaagtga atatatatct
     1561 gtcttaaatg aagaaagaac aaccctctta tcattctcaa tgaatttttt taaaagacta
     1621 tcagtgatag tcttctccgt tttctccccc tcaaaaacaa ataaaatccg ctcagtcatt
     1681 aaatgtaccc gctttataca ttttctctat attatgagct tctcgcaact ctttgtctgt
     1741 tttctcgaaa agtggagtaa tccctttatc atccataatg aagtaacaat caggcctaag
     1801 caactcattc gtcatgacat ttgtattatg cgttgtaatt atcacctggg cgccggcttt
     1861 tttcatctcc ttaacaataa gcatggaaag cgagtgatga taaaaagcat caaactcatc
     1921 tacaaagata aatgaaacac atttttcatc tttaaatcgt tgcaaccagt aataaaaaag
     1981 agctaatgat tttgtacctg tggacgcaac tccatagaat ggaatttgct tactcccaaa
     2041 atcaaagcca atatcttcaa caactccatt attactttga attttcatta cgcaaagttt
     2101 acatttaacc cctgctttat tcaaaaacct ttcaaaatca tcaacattac ctctctccac
     2161 gatatccgga gtgattaggt gtcgccccat ctctagtcca agataattat ttgaatcaag
     2221 agatctgaaa tacaacattt tctcaacaaa aacaataaac tgattaaata gatccttttc
     2281 gataccatca ttaaggatgg cgttattttt tatataatta atgatcgata ttttagactc
     2341 cgcaagagca gtgtttaaag tttctgttcc tgataatgag aaataggcat ttgaatcaag
     2401 cactctatta aatttagtta caagcctgcc attgataaac aactcttcaa aaacaagttc
     2461 tttcacactc cttttcccat ataaataagt tacaatatta tcaccgaatt taaaatcata
     2521 cttaaatctc gcaataccag agttgttaag tgcatttata tagttattat acatgccatc
     2581 attaacatta aactcagtta agtgagcgac aatatcaaaa agagcaagcc ctaagttgct
     2641 tttccctata ccatttttac cgtataccaa tgattttttg acaacaccat caagtataca
     2701 atcttgatta aattcataat tcttcctatg agtaagatca aacactaatt tgtctgaaaa
     2761 ccccttaaac ccctcaactt caaatctgta tatcataaaa gcctcacatc aaagatgccg
     2821 taactatatc atggcaccgt aaaaaaatta caccaaatat agatattgat ttttcttatc
     2881 gctgcaatta aagttgcaag cgaaggctct cgcagtccta tgaaactcag catgcttgct
     2941 gttttttata ggtgtcagtt cctacaactg acgaagacag gagagtacaa aatgaaacgt
     3001 aaaagcgtat tcgttcgtgc ctaccgtcgc tttcgctacg gcgagtggga agacgtatgc
     3061 agtcattacc gctcaatgcc tcgctaaacg acctggctga ccgcgaagag ccttcaatgc
     3121 gtaaaagttt tgtaacttgc cgtgccatac cgatttacca taacgtcaca ttacgcgcac
     3181 cgctaaaacg cgctgaacgc gattctgccg caaacaccgc aaaaagagat gctttccccg
     3241 aggtaaaccg gaaaaatgcg tcaggatcgc tttcggctca ctgcatagct atgcatgaaa
     3301 gtgaatggcg atcggtttgg gagcttacgg cgttcatacc gtctgttttc gacagtttct
     3361 ctccgggaag ctaatctgcc ataagcctgg ataatagggc ccggtgatac tccgtaatag
     3421 ctatcagcac ctccgcatac tctctgtccc cgacacgctt accgtcgata aagagttttt
     3481 tctgcaacgc ccccagtcgc atgacttctt tcagcacccg gtcatcagtc agtgaattaa
     3541 ctttcttacc gagagctgcc gcccgtaaaa aaccagaaac ggtcttgccg cattcagcag
     3601 ccctttttct gatttcctgg tcttcttctg ccgtcagacg aacagggcga ctgatagccc
     3661 gcctgcgcgt attacttcca cttcgttttg tcataaaaca tggctccgta tctgacatgg
     3721 ggtgtcgggg cgaagccctg accagggtaa ttgtaatagc gtgcatgtat gcgcggtata
     3781 acaattgcac atcctgtcct gtctgcaagt tcgaattacc aacaaagcac tgctgttttt
     3841 tggcagtgac agtgttgtct gactgaaatg tccgtcggca gaatacctgc agtaagacgg
     3901 tcgaaaagtg gtgcgcgata taatcacacg acgcagatga cagacagaac ggagaaaaca
     3961 gaaagatgaa caagcagcag caaaccgcac tcaacatggc aaaattcata a
//
