LOCUS       NZ_CP051710             1549 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-124 plasmid pSCU-124-4, complete
            sequence.
ACCESSION   NZ_CP051710
VERSION     NZ_CP051710.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609784
            Assembly: GCF_012934635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1549)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     F plasmids are the primary drivers of antibiotic resistance in
            human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1549)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-APR-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 36x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 02:52:57
            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)                     :: 4,847
            CDSs (total)                      :: 4,738
            Genes (coding)                    :: 4,482
            CDSs (with protein)               :: 4,482
            Genes (RNA)                       :: 109
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 256
            CDSs (without protein)            :: 256
            Pseudo Genes (ambiguous residues) :: 0 of 256
            Pseudo Genes (frameshifted)       :: 166 of 256
            Pseudo Genes (incomplete)         :: 105 of 256
            Pseudo Genes (internal stop)      :: 30 of 256
            Pseudo Genes (multiple problems)  :: 41 of 256
            Pseudo Genes (short protein)      :: 3 of 256
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051710.1.
            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..1549
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-124"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-124-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            456..581
                     /locus_tag="HHJ37_RS23995"
                     /old_locus_tag="HHJ37_24050"
     CDS             456..581
                     /locus_tag="HHJ37_RS23995"
                     /old_locus_tag="HHJ37_24050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001431667.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001431667.1"
                     /translation="MWLPVLFRFLVDSLATLGHRLAASGITSRMLSVIPVLFFWG"
                     /name="hypothetical protein"
     gene            complement(1026..1502)
                     /locus_tag="HHJ37_RS24000"
                     /old_locus_tag="HHJ37_24055"
     CDS             complement(1026..1502)
                     /locus_tag="HHJ37_RS24000"
                     /old_locus_tag="HHJ37_24055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /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_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          33..141
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="100.0"
                     /evalue="4.23e-47"
     Typing          complement(337..435)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          535..795
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 aagccatcat gacacatctg tgcaacacct tgttgcgtgt tgtcgcatcc tggatgcgac
       61 aacgttgtgt catcctggat gcgacaggta aataaaaaac acactaaaaa aacaaccact
      121 tacaaatcgg cgtaaaagat ctattctagg caagggtgtt gcgtgcaacg caacgccctt
      181 tgggggtgtc ggggcgaagc cctgacccag tcacgtagcg atagcggagt gtatactggc
      241 ttactcctat gcaagcctcg ccagccgtga tttttgccag atttcgtggt tttcacgttc
      301 aacagctcca tcgtgttttt gccgtccgtt caccgttaaa acgcctcaga aatcgggaca
      361 ggatgtgtaa tcgtataacc gcgcatgcac gccgatacga ttaccacttg gtcagggctt
      421 caccccgaca ccccgcatca gtgcgtaagt gctcaatgtg gcttccggtt ctcttccgct
      481 tcctcgtcga ttcgctcgct acgctcggtc atcgacttgc ggcgagcggg atcacctctc
      541 gcatgttgtc ggtgatcccg gtgttgttct tttggggatg agtcgccaga tagcccctca
      601 aacgcgctca aaagctctca gacgcacgaa acgggtttta gatgcccgcc agggcatgga
      661 aggcgcgaaa aacgcttaca gaggctctca ggaggtcaag cgcgccgata cccctaacca
      721 ggggctttca ggtcgccagg aaccgcgcca gccccctgca aagcccattt gcacggaaca
      781 ggcagccatg cggttggtag gtggtcgtag accgtcggtg ttgcagcgat gggggtctgg
      841 ggttctcccc agacggtttc cggtagcgct caaggcgctg ccggaaccgt ggcggctcgg
      901 ttttttctgg agaacgggga gcaaaaacac gcaaaggatt ttgaggcggc aaaagagcaa
      961 tgcaggatag acaatcatgg tcagaacgtt aacacgtagc ccctgattgt ccccctgccg
     1021 ctagctcaat ttgaaaacat ggccatgatt cggcgctgaa tatcaccgtc tttgttgacc
     1081 agtgttttag tgacaaacgc tgcatggttt ttcgtagtgt tgtatccctt ccagacttca
     1141 tgtggatcga gggcatacgc acaaacctta ccagcaacgg ggattctaac taatgcattt
     1201 tttgattcta agtaattgag ccaccgaata attgtgcttc tgctaactcc aagtttttca
     1261 gctaggaatt gctgatccgc aacgacagcg ccacacgtag gatcgatatg ctccgctaaa
     1321 aatgagtaca gcttcagtgc tgatatgcct tggctatcct tcagcagctc tcgaacacgt
     1381 tcccaacctt ttggggatac ctgtgtaaac cttgaatttt tctttgcttc ttcgagatcc
     1441 tcggtgtttt tctttgcctc atctgaaagt tgtttcagtc gtttttctga atcaataaac
     1501 atgatttttt ccctctgaaa atcccatgca ctaacgttgg ttcaaatct
//
