LOCUS       NZ_CP023958             3264 bp    DNA     circular CON 14-JUN-2024
DEFINITION  Escherichia coli strain FDAARGOS_448 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP023958
VERSION     NZ_CP023958.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07312492
            Assembly: GCF_002591135.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3264)
  AUTHORS   Croxen,M., Tallon,L.J., 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  JOURNAL   Unpublished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 3264)
  AUTHORS   Croxen,M., Tallon,L.J., 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                   :: Celera v. 8.2, SPAdes v. 3.6.0
            Genome Coverage                   :: 741.955x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002591135.1-RS_2024_06_14
            Annotation Date                   :: 06/14/2024 04:47:32
            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)                     :: 5,309
            CDSs (total)                      :: 5,184
            Genes (coding)                    :: 4,966
            CDSs (with protein)               :: 4,966
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 218
            CDSs (without protein)            :: 218
            Pseudo Genes (ambiguous residues) :: 0 of 218
            Pseudo Genes (frameshifted)       :: 86 of 218
            Pseudo Genes (incomplete)         :: 140 of 218
            Pseudo Genes (internal stop)      :: 49 of 218
            Pseudo Genes (multiple problems)  :: 48 of 218
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023958.1.
            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..3264
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_448"
                     /isolation_source="Urine"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_448"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2014-08"
                     /collected_by="BC Centre for Disease Control"
     gene            complement(join(3185..3264,1..115))
                     /locus_tag="CRN68_RS00365"
                     /old_locus_tag="CRN68_00365"
     CDS             complement(join(3185..3264,1..115))
                     /locus_tag="CRN68_RS00365"
                     /old_locus_tag="CRN68_00365"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041643.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            388..711
                     /gene="mobA"
                     /locus_tag="CRN68_RS00370"
                     /old_locus_tag="CRN68_00370"
     CDS             388..711
                     /gene="mobA"
                     /locus_tag="CRN68_RS00370"
                     /old_locus_tag="CRN68_00370"
                     /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"
     gene            complement(919..1497)
                     /locus_tag="CRN68_RS00380"
                     /old_locus_tag="CRN68_00380"
     CDS             complement(919..1497)
                     /locus_tag="CRN68_RS00380"
                     /old_locus_tag="CRN68_00380"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_052266651.1"
                     /translation="MKSEIELKKTEHSSVEIPERILAIWGRSILNSGWTSVPNELLKNQ
                     SKLGIGNTELVLLINLISFMHHPDARVYPSISLLCERMNQDRRTIQRNLNKLVEMDILR
                     IKIRSTGKNSKGMTNLYDITPLMLKLINLKIPSLNTPDEKHTCPKCGKIAISREEITKE
                     FGFRTDTNGKMRTQSWCKDCRGRKIADLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            1894..2349
                     /locus_tag="CRN68_RS00385"
                     /old_locus_tag="CRN68_00385"
     CDS             1894..2349
                     /locus_tag="CRN68_RS00385"
                     /old_locus_tag="CRN68_00385"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_039023474.1"
                     /translation="MTTKFNKFELHSAFRDGKLNEKYFVDLPYLKEEQRRALASFLGAI
                     TREEPLPGKNKPSWLDDNSIKISGTDAYEDGNYWHYHCGPYPEGVKLRSMTFNLGMNVA
                     GLTSAEVIHYQKLNDGTVFVVGFSPTHEPFPKSDAPHYNPLFTESDD"
                     /name="hypothetical protein"
     Typing          153..379
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="99.0"
                     /evalue="6.34e-74"
     Typing          complement(2626..3156)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.888"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          389..708
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.74e-63"
ORIGIN
        1 cacacatggc ggcctgctcg tcagcatcga gtgcgtccag tttttcgagc agcgtcaggc
       61 tctggctttt tatgaatccc gccatgttga gtacagtttg ctgctgcttg ttcatctttc
      121 tgttttctcc gttctgtctg tcatctgcgt cgtgtgatta tatcgcgcac cacttttgga
      181 ccgtcttacc gccggtattc tgccgacgga catttcagtc agacaacact gtcactgcca
      241 aaaaaacagc agtgctttgt tggtaattcg aacttgcaga caggacagga tgtgcaattg
      301 ttataccgcg catacatgca cgctattaca attaccctgg tcagggcttc gccccgacac
      361 cccatgtcag atacggagcc atgttttatg acaaaacgaa gtggaagtaa tacgcgcagg
      421 cgggctatca gtcgccctgt tcgtctgacg gcagaagaag accaggaaat cagaaaaagg
      481 gctgctgaat gcggcaagac cgtttctggt tttttacggg cggcagctct cggtaagaaa
      541 gttaactcac tgactgatga ccgggtactg aaagaagtta tgagactggg ggcgttacag
      601 aaaaaactct ttatcgacgg caagcgtgtc ggggacaggg agtatgcgga ggtgctgatc
      661 gctattacgg agtatcaccg tgccctgtta tccaggctta tggctgatta gcttcccgga
      721 gagaaactgt cgaaaacaga cgatatgaac gccgtaagcc cccaaaccga tcgccattca
      781 gtttcatgca tagtcatgca acgcgctgaa aacaatcctg acgcattttt ccggtttacc
      841 ccggggaaaa catctctttt tgcggtgttt gcggcagaat cgcgttcagc gcgtttctgc
      901 ggtgcgcgta atgcgacgtt atggtaaatc cgcaattttc ctacctcgac aatccttgca
      961 ccaactttgc gttctcatct tcccattagt gtcagttctg aatccaaact cctttgttat
     1021 ttcttctctt gatatggcta tttttccgca ttttggacac gtatgttttt catcgggcgt
     1081 atttaaagat ggtattttta ggttgattaa cttcagcatt aaaggggtta tgtcatacaa
     1141 gttagtcatt cctttagagt ttttgccggt ggagcgtatt tttatcctca gaatgtccat
     1201 ttctactaac ttgtttaaat ttctctgaat tgttcgtctg tcctgattca ttctttcgca
     1261 tagaagtgaa attgatgggt acactcttgc gtcaggatga tgcatgaaag atatcagatt
     1321 aatcaaaagt acaagctctg tgtttcctat tcctagctta gattggtttt ttaatagttc
     1381 attggggacg gatgtccagc cagagtttaa aatgctgcgc ccccatatgg ctaagatcct
     1441 ttctgggatc tctactgatg agtgttctgt ttttttgagt tcgatttctg atttcaattt
     1501 ctgtcaccaa tcataataac aatacctata tatataggta ttgttattat gatttattat
     1561 ttgggcggca tcaatgccgc cctttaattt gaccaaaaag gcctaatgtc tagcactggg
     1621 aaaggacctc tcttaccatc taattgagta agattttatc ttcccagact tcttcaaaca
     1681 taggactgac atgttggcaa acgtacgatt tgataatcac agctgcgata cagaacgtcg
     1741 tcagcagtac aaatctcgtg ctgacgaagt gctgctctcg cgttcataca agaatcaggc
     1801 acatgaagcg ttaaaatgcg attctccgca gtctgatgaa tcgatctttg atatgctatc
     1861 tacttactca gtaaggtaag tggaaagtgt ttgatgacaa ccaaattcaa taagtttgag
     1921 cttcattcgg ctttccgaga cgggaagctg aatgaaaagt atttcgtaga tttaccctac
     1981 ctcaaagaag agcaacgccg ggcattagcc tctttcttgg gtgcgataac tcgtgaagag
     2041 cctcttccag ggaaaaacaa gccttcatgg cttgatgata attccattaa aatttccggt
     2101 actgatgcgt acgaagacgg gaactattgg cattatcatt gcggtccata tccagaaggg
     2161 gtcaaactta gatcgatgac ttttaacttg ggtatgaacg ttgcggggct aacctccgct
     2221 gaagtgatcc actatcaaaa actcaacgat ggcacggtgt ttgtcgtagg cttctcccct
     2281 acacatgagc ccttccctaa gtctgatgcg ccgcattaca acccactctt cactgaatca
     2341 gatgattaaa tatctgaata gtggctggta aggatatgtt gagatttttt tctctcagct
     2401 gtagtctctt ttcctgaaac gaaaaaacca cctggggagg tggtttttcg aaggttcagt
     2461 aagttgggga acttctgaac cgtggtaaca gtcttgtgcg agacatgtca ccaaatctgt
     2521 cctttcagtg tagccgcagt caggccatca cttcaagaac tctcgataca tctctcgcac
     2581 atcctgtcta ccaatggccg cagccaatgg cgataagtcg tgtctttccg ggttggactc
     2641 aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca
     2701 gcccagcttg gagcgaacga cctacaccga actgagatac caacagcgtg agctatgaga
     2761 aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg
     2821 aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt
     2881 cgggtttcgc cacctctgac ttgagcgtcg gtttttgtga tgctcgtcag gggggcggag
     2941 cctatggaaa aacgccaacg gcgcggcctt tgtccctggc ttcggctttt tgctcacatg
     3001 ttctttccgg cgttatcccc tgattctgtg gataaccgta ttaccgcctt tgagtgagct
     3061 gacaccgctc gccgcagtcg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa
     3121 gagcgcctta tgtgacattt tctccttacg ctctgttgtg ccgttcggca tcctgccctg
     3181 agcgttatat ctctgtgcta ttttctactt caaagcgtgt ctgtatgctg ttctggagtt
     3241 cttctgcgag ttcgtgcagc ttct
//
