LOCUS       CP054324                2113 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-390 plasmid pSCU-390-5, complete
            sequence.
ACCESSION   CP054324
VERSION     CP054324.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609796
KEYWORDS    .
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., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  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  JOURNAL   Unpublished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., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 13x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:17:01
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,020
            CDSs (total)                      :: 4,901
            Genes (coding)                    :: 3,691
            CDSs (with protein)               :: 3,691
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 1,210
            CDSs (without protein)            :: 1,210
            Pseudo Genes (ambiguous residues) :: 0 of 1,210
            Pseudo Genes (frameshifted)       :: 1,101 of 1,210
            Pseudo Genes (incomplete)         :: 108 of 1,210
            Pseudo Genes (internal stop)      :: 59 of 1,210
            Pseudo Genes (multiple problems)  :: 54 of 1,210
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..2113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-390"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-390-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            complement(join(1909..2113,1..62))
                     /locus_tag="HHJ49_25095"
     CDS             complement(join(1909..2113,1..62))
                     /locus_tag="HHJ49_25095"
                     /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="QKN36158.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     gene            complement(66..1031)
                     /locus_tag="HHJ49_25100"
     CDS             complement(66..1031)
                     /locus_tag="HHJ49_25100"
                     /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="QKN36157.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     Typing          complement(407..638)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 cttcttaaaa aaaataaacc aatagtctta tttccattca ggtattcaat attaatattc
       61 atacgttaat ccgatttatc cttctcaggg gcgcgtttgt aacgccgttt acctgaatcc
      121 cagacaaacg ccgtccgctt cccgtcatca gtgccatccc ctacatcgtc ggcaatgaca
      181 agatcctcat tggtttctcg atccaactgg aggacgtttt ttagcgcccc accggtcgag
      241 ataaaacggc gcttgtgaag ctgccgcgtc agctcaagaa accactcagg atcgtttgcc
      301 atatcttccg gtttaacgga gtatttcagc gtttcagcaa ccgcgctttg cagttgctcg
      361 gcaacgttgg ccacaacctc acctgtctta gtttttactg cccgaatatc gatattcggc
      421 tcatagttca cccgcaagca atcgcgccag agttctaccc aacgttcgtg cttaacgtag
      481 ttcttccctt taaaccaaga aggttgcacc atcagcagac agtgaaaatg cggatgtgcg
      541 ctgccatcct tacctcgcgt cacctccgta gccctgatcc acccctgaac aggtgatagc
      601 tcctttcgct tttccattcg cttaaacgcc gcattcattg ctgtaaggac tgttccaagt
      661 tcacctatct cgcagttcct gacagttaac gtcagaaaca accatcggga agacgggtaa
      721 tccacaacga ttttcggtag agcctgataa aaacgggctt gccacatgag ggttcttctc
      781 cactggcaga cagggcaatg acggacacgg caaaattgcg cactacgaag ccgtaggcgc
      841 gtttctccgg tttccatgat ggtagaccaa ccaaaacgta acaaaccgct acaggaggcc
      901 atacggagtg catagcgctc gaattcagca gcagtctggt agataccccc gacagaatcg
      961 gtaagcgtgc gctgggtatc ccaaactgca tcacgggggc tgtagtccga aaggaattta
     1021 tcttctgaca ttaagcctgc tccgatctgg gcaggctgtg atttgatgtg gtatattcat
     1081 cacgtacctg tgcattgcga gccagtacat gtcaccagag tttgccgctg aggtgacaca
     1141 ttcgaaatgt tggggagtgt tgacgcactc cccaacgccg attaaaaacg cctcaattct
     1201 gctccatttt ctttgacctg tcaaaaccca ctcaaagcct cgtcattact gggctaaacc
     1261 actatttcat atccgccatt tatcccttaa gtataaatac aaggatcacg cgcgagaatt
     1321 gcgcaaaaaa taaccacaat tttaaccccc caaaacaagc acccccgaac ggcttacccc
     1381 aaccttttcc acacacccga tcaccaaaac agggaataaa aacaaaaccc tgtcttacag
     1441 gtggatggcc tcacttcgtg aaaccatcca ccccgcataa gttttttaat cggtggtgtc
     1501 gtcaatcact aaatcggaac cccaaagggg acccccacga tttagcattt gacgagatta
     1561 actctcggag atggcatcat gcttttaacg gactttaaaa aacggtgaac ggatgcggat
     1621 tttaatccgt gtctgtgagg cgttgagcaa cgagcaaagc gaggcggtag aaagagagcc
     1681 agcggcaggc tcaggacgat aatccgggga aaatgtacca ctcgcagagt gttaacattt
     1741 gacatcggat tgtctatcct gcattggtgt cgagttggca aggctgagga taatgctgag
     1801 gataatgctg aggataatgc tgaggataat gcaggataga cagagcacta gagattgcat
     1861 gcaatctcgt acctatcacc tcagcctgcc gctggctctt ttccagaact aagaatgcgt
     1921 tcttaaaaat ccaaacttga taccgtttaa atctattttc acaaaaagag tttttaccct
     1981 ctcgtttgtt ttctgaatat ataaaattaa ttcatcctca aaaccttcgt gcggatgaaa
     2041 accaaatgtg ccaaaactta atccatcaat aagcaaaata aggtttttaa acctgtcagg
     2101 aatcaccgct tca
//
