LOCUS       NZ_CP054361             2113 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-172 plasmid pSCU-172-8, complete
            sequence.
ACCESSION   NZ_CP054361
VERSION     NZ_CP054361.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943545
            Assembly: GCF_013315695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2113)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Title: F plasmids are the major carriers of antibiotic resistance
            genes in human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2113)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-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                   :: 78x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:55:40
            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)                     :: 5,461
            CDSs (total)                      :: 5,339
            Genes (coding)                    :: 5,056
            CDSs (with protein)               :: 5,056
            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)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 85 of 283
            Pseudo Genes (incomplete)         :: 198 of 283
            Pseudo Genes (internal stop)      :: 39 of 283
            Pseudo Genes (multiple problems)  :: 33 of 283
            Pseudo Genes (short protein)      :: 3 of 283
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054361.1.
            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..2113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-172"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-172-8"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            join(1964..2113,1..117)
                     /locus_tag="HPE50_RS26955"
                     /old_locus_tag="HPE50_26965"
     CDS             join(1964..2113,1..117)
                     /locus_tag="HPE50_RS26955"
                     /old_locus_tag="HPE50_26965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     gene            995..1960
                     /locus_tag="HPE50_RS26960"
                     /old_locus_tag="HPE50_26970"
     CDS             995..1960
                     /locus_tag="HPE50_RS26960"
                     /old_locus_tag="HPE50_26970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     Typing          1389..1620
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 ggttttgagg atgaattaat tttatatatt cagaaaacaa acgagagggt aaaaactctt
       61 tttgtgaaaa tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc
      121 tggaaaagag ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg
      181 ctctgtctat cctgcattat cctcagcatt atcctcagca ttatcctcag cattatcctc
      241 agccttgcca actcgacacc aatgcaggat agacaatccg atgtcaaatg ttaacactct
      301 gcgagtggta cattttcccc ggattatcgt cctgagcctg ccgctggctc tctttctacc
      361 gcctcgcttt gctcgttgct caacgcctca cagacacgga ttaaaatccg catccgttca
      421 ccgtttttta aagtccgtta aaagcatgat gccatctccg agagttaatc tcgtcaaatg
      481 ctaaatcgtg ggggtcccct ttggggttcc gatttagtga ttgacgacac caccgattaa
      541 aaaacttatg cggggtggat ggtttcacga agtgaggcca tccacctgta agacagggtt
      601 ttgtttttat tccctgtttt ggtgatcggg tgtgtggaaa aggttggggt aagccgttcg
      661 ggggtgcttg ttttgggggg ttaaaattgt ggttattttt tgcgcaattc tcgcgcgtga
      721 tccttgtatt tatacttaag ggataaatgg cggatatgaa atagtggttt agcccagtaa
      781 tgacgaggct ttgagtgggt tttgacaggt caaagaaaat ggagcagaat tgaggcgttt
      841 ttaatcggcg ttggggagtg cgtcaacact ccccaacatt tcgaatgtgt cacctcagcg
      901 gcaaactctg gtgacatgta ctggctcgca atgcacaggt acgtgatgaa tataccacat
      961 caaatcacag cctgcccaga tcggagcagg cttaatgtca gaagataaat tcctttcgga
     1021 ctacagcccc cgtgatgcag tttgggatac ccagcgcacg cttaccgatt ctgtcggggg
     1081 tatctaccag actgctgctg aattcgagcg ctatgcactc cgtatggcct cctgtagcgg
     1141 tttgttacgt tttggttggt ctaccatcat ggaaaccgga gaaacgcgcc tacggcttcg
     1201 tagtgcgcaa ttttgccgtg tccgtcattg ccctgtctgc cagtggagaa gaaccctcat
     1261 gtggcaagcc cgtttttatc aggctctacc gaaaatcgtt gtggattacc cgtcttcccg
     1321 atggttgttt ctgacgttaa ctgtcaggaa ctgcgagata ggtgaacttg gaacagtcct
     1381 tacagcaatg aatgcggcgt ttaagcgaat ggaaaagcga aaggagctat cacctgttca
     1441 ggggtggatc agggctacgg aggtgacgcg aggtaaggat ggcagcgcac atccgcattt
     1501 tcactgtctg ctgatggtgc aaccttcttg gtttaaaggg aagaactacg ttaagcacga
     1561 acgttgggta gaactctggc gcgattgctt gcgggtgaac tatgagccga atatcgatat
     1621 tcgggcagta aaaactaaga caggtgaggt tgtggccaac gttgccgagc aactgcaaag
     1681 cgcggttgct gaaacgctga aatactccgt taaaccggaa gatatggcaa acgatcctga
     1741 gtggtttctt gagctgacgc ggcagcttca caagcgccgt tttatctcga ccggtggggc
     1801 gctaaaaaac gtcctccagt tggatcgaga aaccaatgag gatcttgtca ttgccgacga
     1861 tgtaggggat ggcactgatg acgggaagcg gacggcgttt gtctgggatt caggtaaacg
     1921 gcgttacaaa cgcgcccctg agaaggataa atcggattaa cgtatgaata ttaatattga
     1981 atacctgaat ggaaataaga ctattggttt atttttttta agaagtgaag cggtgattcc
     2041 tgacaggttt aaaaacctta ttttgcttat tgatggatta agttttggca catttggttt
     2101 tcatccgcac gaa
//
