LOCUS       NZ_CP051724             1538 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-116 plasmid pSCU-116-5, complete
            sequence.
ACCESSION   NZ_CP051724
VERSION     NZ_CP051724.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609778
            Assembly: GCF_012934555.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1538)
  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  JOURNAL   Unpublished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 1538)
  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                   :: 21x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 01:49:14
            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)                     :: 5,046
            CDSs (total)                      :: 4,924
            Genes (coding)                    :: 4,721
            CDSs (with protein)               :: 4,721
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 62 of 203
            Pseudo Genes (incomplete)         :: 141 of 203
            Pseudo Genes (internal stop)      :: 43 of 203
            Pseudo Genes (multiple problems)  :: 41 of 203
            Pseudo Genes (short protein)      :: 4 of 203
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051724.1.
            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..1538
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-116"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-116-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(996..1472)
                     /locus_tag="HHJ31_RS24980"
                     /old_locus_tag="HHJ31_24995"
     CDS             complement(996..1472)
                     /locus_tag="HHJ31_RS24980"
                     /old_locus_tag="HHJ31_24995"
                     /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          14..122
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(311..392)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          507..764
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="99.0"
                     /evalue="8.44e-113"
ORIGIN
        1 gtgcaacacc ttgttgcgtg ttgtcgcatc caggatgcga caacgttgtg tcaccctgga
       61 tgcgacaggt aaacaaaaaa cacactaaaa aaacaacaac ttacaaatcg gcgtaaaaga
      121 tctattctag gcaagggcgt tgcgcgcaac gcaacgccct tttggggtgt cggggcgaag
      181 ccctgaccca gtcacgtagc gatagcggag tgtatactgg cttactcctc tgcaagcctc
      241 gtcagccgtg attttgcccg atttcgcgct ctccacgctc gatcatgttt ttgccgtccg
      301 ttcaccgtta aaacgcctca gaaatcggga caggatgtgg gaatgtcgga ccgcgcacgc
      361 gcactcagac attccccact tggtcagggc ttcaccccga caccccgcat ccgtgcgtaa
      421 gtgctcaatg taacttccgg ttctcttccg cttcctcgtc gattcgctcg ctacgctcgg
      481 tcatcgactt gcggcgagcg ggatcacctc tcgcatgttg tcggtgatcc cgttgttgtt
      541 ctttcgggga tgagtcgtca gatagccctt caaacacgct cagaagctct cagacgcacg
      601 aaacgggttt aaatgcccgc cagggcatgg aaggcgcgaa aaacgcttac agaggctctc
      661 aggaggtcag gcgcgccgat acccctaacc aggggctttc aggtcgccag gaaccgcgtc
      721 agctccctgc aaagcctatt tgcagggcac aggcagctat tcggctggtt ggtggtcgta
      781 gaccgtcggt gttacagcga tgggggtctg gggttctccc cagacggttt ccggttgcgc
      841 tcaaggcgca gccggaaccg tggcggcgcg gtcgttctgg ggatcgggga gcaaaaacac
      901 gcaagggatt ttgaggcggc aaaagagcaa tgcaggatag acaatcatgg tcaaaacgtt
      961 aacacgtagc ccctgattgt ccgcctgccg ctggctcaat ttgaaaacat ggccatgatt
     1021 cggcgctgaa tatcaccgtc tttgttgacc agtgttttag tgacaaacgc tgcatggttt
     1081 ttcgtagtgt tgtatccctt ccagacttca tgtggatcga gggcatacgc acaaacctta
     1141 ccagcaacgg ggattctaac taatgcattt tttgattcta agtaattgag ccaccgaata
     1201 attgtgcttc tgctaactcc aagtttttca gctaggaatt gctgatccgc aacgacagcg
     1261 ccacacgtag gatcgatatg ctccgctaaa aatgagtaca gcttcagtgc tgatatgcct
     1321 tggctatcct tcagcagctc tcgaacgcgt tcccaacctt ttggggatac ctgtgtaaac
     1381 cttgaattct tctttgcttc ttcgagatcc tcggtgtttt tctttgcctc atctgaaagt
     1441 tgtttcagtc gtttttctga atcaataaac atgatttttt ccctctgaaa atcccatgca
     1501 ctaacgttgg ttcaaatcta agccatcatg acacatct
//
