LOCUS       CP054338                6211 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-120 plasmid pSCU-120-3, complete
            sequence.
ACCESSION   CP054338
VERSION     CP054338.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609780
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6211)
  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  JOURNAL   Unpublished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 6211)
  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                   :: 35x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:46:26
            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)                     :: 5,323
            CDSs (total)                      :: 5,202
            Genes (coding)                    :: 4,211
            CDSs (with protein)               :: 4,211
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 991
            CDSs (without protein)            :: 991
            Pseudo Genes (ambiguous residues) :: 0 of 991
            Pseudo Genes (frameshifted)       :: 886 of 991
            Pseudo Genes (incomplete)         :: 117 of 991
            Pseudo Genes (internal stop)      :: 48 of 991
            Pseudo Genes (multiple problems)  :: 54 of 991
            CRISPR Arrays                     :: 2
            ##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..6211
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-120"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-120-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            complement(512..952)
                     /locus_tag="HHJ33_26495"
     CDS             complement(512..952)
                     /locus_tag="HHJ33_26495"
                     /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="entry exclusion protein 1"
                     /protein_id="QKN47611.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            1170..1559
                     /locus_tag="HHJ33_26500"
     CDS             1170..1559
                     /locus_tag="HHJ33_26500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN47612.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            1603..2142
                     /locus_tag="HHJ33_26505"
     CDS             1603..2142
                     /locus_tag="HHJ33_26505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="QKN47613.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFGVVCGKGRNPTLRLWPAIFSGEIDVFPG
                     DRRSRLISSMTSVAPA"
                     /name="IS91 family transposase"
     gene            complement(2114..2950)
                     /locus_tag="HHJ33_26510"
     CDS             complement(2114..2950)
                     /locus_tag="HHJ33_26510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="QKN47614.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(2950..3753)
                     /gene="aph(3'')-Ib"
                     /locus_tag="HHJ33_26515"
     ARG             complement(2954..3753)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(3814..4629)
                     /gene="sul2"
                     /locus_tag="HHJ33_26520"
     ARG             complement(3818..4629)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(5089..5247)
                     /locus_tag="HHJ33_26525"
     CDS             complement(5089..5247)
                     /locus_tag="HHJ33_26525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001314450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QKN47617.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="replication initiation protein"
     gene            complement(5289..5693)
                     /locus_tag="HHJ33_26530"
     CDS             complement(5289..5693)
                     /locus_tag="HHJ33_26530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012579059.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication initiation protein"
                     /protein_id="QKN47618.1"
                     /translation="MLHVAGEKRQHRRVSRICDTGDIPLPRSLTRYARSFGCGERYRLT
                     DGDGNFLEDTRKTLSKEEIRPRRSRFSIGSAPLTSIAKSDAQISGGETRQDYKDPRRFP
                     LVAPSCALLFLPFGLPVSFRCYGRGFSFHA"
                     /name="plasmid replication initiation protein"
     gene            5818..5967
                     /locus_tag="HHJ33_26535"
     CDS             5818..5967
                     /locus_tag="HHJ33_26535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN47619.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             complement(2118..2950)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          5610..5783
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(5081..5686)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaaaagcg ttcctcactg tatcgttcat gcctgcatga acgggttatt cttcctgact
       61 acagaattac atcgctcctt cagttcatac atcacttata catcactttt acatcactta
      121 tacatcactt ttacatcatt ccttcagctc atacgtcact ttcatcctct gtgccatttg
      181 tacatcaccc ccttcctgaa cgtgctgaca gcgggttttc cggctgcgcc ggcaacgctt
      241 cacggccacg caataaattg cgtccccgtt caccgttttc ggatgggaag aacgccggaa
      301 acaggactta ccccggctga atggtgtgaa tttccgcgct atgcacttgt gcgcatactc
      361 atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc
      421 tgttttaccg gtttcccgtc agaaacgccc tgagggcctc tcaggcggtg ctgataacag
      481 atgttatggt aaatcagagt cacctgcact gttactctga accggagcga aacagccgcg
      541 accagaatcc ccgctttttt tcctgtgcca gcgcgtcagc cagacggcta atttcggcct
      601 gtagttgttc cctctcctca tttcgcaggc ggttttctgc ttcccgcgcc atcttgtctt
      661 caagcattag ggtaacagtc tgctgcagag cgtccagttt ctgctgaatg acgtctagct
      721 gagcattttc cgcctggcta acgacagatt tggagtgtcc ctccttgtgc ctttttggtg
      781 tctcagaagt gcgcagctcg ccataggccc gaatcagttc actggtctcg aactcccggc
      841 gatcattttt tcctgtgcga tagctgacaa ggcctttagc catgtcacga tataattgcg
      901 agcgcgactt tcctgttaat ttcagtgtct cttgaactgt gtgccatgcc ataaaagtga
      961 cagtgtctcc tgtgtgtacc gtattgtaac agcagaacat attactgttt taacacaaaa
     1021 ggtctgaggc tgcccgtgag gcgtgaaaaa tacacaaaaa acctgttgac ggtgtggttt
     1081 tgacgggcgt agtatttcga atactgtata taaacacatt gttataaata cagtttttgc
     1141 tgtttttaaa agtcaaagag gataatttta tgagtacaga gttaaatagc ggtactgtcg
     1201 gtggttttgg tcacatggga ccaaatgacc cctacaatga tggtcatagc ggctctggaa
     1261 gttcgggagg tagttttaac ggtggtggta atggtggcca tgataatagt agtggttcat
     1321 cttatactgc atcctttggt ctcatcactg gccgacaccc gataactgtc ccaggtacga
     1381 agaatattaa ttctgtcgat ctttctgctg tcattaataa cattatacat catgaaggtg
     1441 cacgcaataa catgtaccta gatactgcga acaatgtaag agtgggagtg acgggcactg
     1501 gctggcaatg tctagcaacg gcaggcattt cggctgaggg taaaagaact ttccgctaag
     1561 cgatagactg tatgtaaaca cagtattgca aggacgcgga acatgcctca tgtggcggcc
     1621 aggacggcca gccgggatcg ggatactggt cgttaccaga gccaccgacc cgagcaaacc
     1681 cttctctatc agatcgttga cgagtattac ccggcattcg ctgcgcttat ggcagagcag
     1741 ggaaaggaat tgccgggcta tgtgcaacgg gaatttgaag aatttctcca atgcgggcgg
     1801 ctggagcatg gctttctacg ggttcgctgc gagtcttgcc acgccgagca cctggtcgct
     1861 ttcagctgta agcgtcgcgg tttctgcccg agctgtgggg cgcggcggat ggccgaaagt
     1921 gccgccttgc tggttgatga agtactgcct gaacaaccca tgcgtcagtg ggtgttgagc
     1981 ttcccgtttc agctgcgttt cctgtttggg gtcgtttgcg ggaaggggcg gaatcctacg
     2041 ctaaggcttt ggccagcgat attctccggt gagattgatg tgttcccagg ggataggaga
     2101 agtcgcttga tatctagtat gacgtctgtc gcacctgctt gatcgcggcc gcgatagcta
     2161 gatcgcgttg ctcctcttct ccatccgcgt tccaagctgc ggaaaggcac ccataagcgt
     2221 acgcctggtc gagcaggcga cgcggatcga cgtccagcgc acgagagaat gcgtccgcca
     2281 tctgtgcaat gcgtctagga tcgagacaaa ggtcgtctct gtcagccgga tcgtagaaca
     2341 tattggcggc gccaaagccc acttcaccga ccagaccgac gggatctatc accagccagc
     2401 cgcgactgga gaacatgatg ttttcatgat gcagatcgcc atgtagccca cgcagttccg
     2461 aggcattgct catcatttga tcggctataa tcgccgcgtg gacgtagtca gtttgacaac
     2521 ctgcgttttg atcatcgcgc gcccgctgaa acaaagctgc aaagcgatcc cggatcggga
     2581 gaagggcaga aggcaggggt tcctcagatg cggcatacag cttcgccatt agttccgctg
     2641 caatttcggt cgcctggtag tcgccgtgct cggcaacgat gtgagagagc attcgctccc
     2701 cggcatattc gagcaacatc agattgttct cacgaccgag caaccggact gctcccctcc
     2761 cattgcgcca taccagatag tcggccccgc gcagttcatc agcaatgtct tctataggtt
     2821 tcaatccctt gacgattgca ggagtcccgt ctggcaatga aactttccaa acgaggctgg
     2881 aaaaggtgtc cgcaatgaga acaggttgcg aaacgtgcca atgagcagga aaaacaggcg
     2941 gcatgaacat caaccccaag tcagagggtc caatcgcaga tagaaggcaa ggcgttcgcg
     3001 gtcgggggct tcgatcccca atacattgaa taggacagcg aaggcgcgct ctgcttcatc
     3061 tggcgctgcc cagttctctt cggcgttagc aatcatgagt gccaaatcgg catagcgatc
     3121 tgctgttccg agccgcccaa ggtcgatcag acccgtgcat tgaagagttt tagggtccac
     3181 catgaagttc ggcatgcagg gatcaccatg gcaaacaacc atatcggtgc gctcttggtc
     3241 gagccgcacc ggtagctctc gttcgacacg agccaaaaga tcgagctgcg gcgtactctt
     3301 gtcctcgtcc ggtaagaagt cgggattgac ggcattgcgg gacaccacat caacggcgcg
     3361 tccgaacatt cgcgacagcc tgcgctcaaa cggacattga tcaaccgata ggctgtgaac
     3421 agcgccaagt tgctgcccca ttgacggcca cgctttgagc aaatccgctc cagacagatc
     3481 agccgccggt actcccggaa ttgccgttat caccaagcat gcaccctcct gttcctcctg
     3541 ccagttgatg acctcggggc aagccacacc tcgacctttg agccaaatga ggcggtcacg
     3601 ctctccagcg agctcaccgc ggcgggaagc aggtgcgatt ttcgcgaagg catgcccgtc
     3661 accacgtcga aaaacaaaat caccagattc tccgcctctg acaggcaacc agtcagaatg
     3721 cgattcacca aaaaaaatat tagttcgatt caatggaggt tccttcagtt ttctgatgaa
     3781 gcgcgaatat agagaaatat cccgaatgtg cagttaacga attcttgcgg tttctttcag
     3841 cgccgccaat accgccagcc cgtcgcgcaa ggggcgcggc tcgtgtgtgc ggatgaagtc
     3901 agctccacct gcggcggcgg caagctctgc agcgagtgtc gcggccccga catcccccgg
     3961 accacggcct gtgagcgcgc gcagaaagga tttgcgcgaa acagacagaa gcaccggcaa
     4021 atcgaagcgc agccgcaatt catcgaaccg cgccagcacc gagagcgagg tttcgggagc
     4081 agcccccaga aaaaacccca tgccgggatc aaggacaagg cggttgcgtt tgataccggc
     4141 acccgtcagc gccgcgatgc gcgcgtcaaa gaacgccgca atgtgatcca tgatgtcgcc
     4201 agcgggtgcc tcgcgccgat ctgcctgccc gtcttgcacc gaatgcataa cgacgagttt
     4261 ggcagatgat ttcgccaatt gcggatagaa cgcagcgtct ggaaaaccgc gaatatcatt
     4321 gagataggcc acaccacgcg acaaggcata ggcttgcgtc gcgggttgat aactgtcgag
     4381 cgagacggga atgccatctg ccttgagcgc gtccagcacc ggcgcgatac gcgcgatttc
     4441 tgtgtcggac gaaacaggcg cggcgtcggg attgctggat gccggaccga ggtcgatcac
     4501 atctgccccc tcggccatca gcttacgcgc ctgcgcaatg gctgcgtctg gcgccagata
     4561 ccggcctcca tcggagaaac tgtccgaggt tatgttgacg atgccgaaaa tgatgagcga
     4621 tttattcatg ggggcttcta taataataat aatcgagcat gagtctcata cggatgctcg
     4681 ggtcgaaagg gaatccccag gcgagtaacc tgtttgcggt gatccgtttc atgatgatgt
     4741 atctgtagca ttttggaaat aaatatatca tctctcaata agtagatata tttatctttt
     4801 ttgcttcttt ggtgctgcaa gtcaccaata cgagggaaac ctgttacgga gcggtttaac
     4861 cgtaatcaac agtgactggt gtcatgttcg gaagattaat tgatagtaat ctacaaagga
     4921 tcttcttgag atccttttca atgaatcgta atctcttgct ctgtaaacga aaaaaccgcc
     4981 tggggaggcg gtttgttcga aggttaagtc agttggggaa ctgcttaacc cggtaacagg
     5041 gttcacgaga ccgccattac caaaactgtt ctttcagtgt agccgcagtc aggcctctac
     5101 ttcaagacct cttaatctat cttctcgtgc actcctgtta ctaatggctg ctgccagtgg
     5161 cgttttgtcg tgtctttccg ggttggactc aagttgatag ttaccggaca aggcgcagcg
     5221 gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaactg ccttcacgga
     5281 actgagtgtc aggcgtggaa tgagaaaccg cggccataac agcggaatga caccggtaaa
     5341 ccgaaaggca ggaacaggag agcgcacgag ggagctacca gggggaaacg cctgggatct
     5401 ttatagtcct gtcgggtttc gccaccactg atttgagcgt cagattttgc gatgcttgtc
     5461 aggggggcgg agcctatgga aaaacggctt cgccgtggcc ttatctcttc tttgctaagt
     5521 gtcttcctgg tatcttccag gaaatttccg tccccgtccg taagccggta ccgctcgccg
     5581 cagccgaacg accgagcgta gcgagtcagt gagcgaggaa gcggaatatc tcctgtatcg
     5641 catattctgc tgacgcgccg gtgctgcctt ttttctcctg ccacatgaag cacttcactg
     5701 attttcgcaa tcgtggcaac atagtaagcc agtatacact ccgctagcgc tacatgactg
     5761 gttcagggct gcgccccgaa acccgctaac aacctctcag ctactggata tcaccccatg
     5821 ccatctgaat atgatgaaca actggattcg actgatacgc agcttcccgg cgaatatgac
     5881 ctttttgatt taatggcgca ggttactgaa gagaacctgc atgcccctgt ggattttggg
     5941 tcgcctgtcg gccgggaagc gttatagctt tttcgcttgc ccgcgtacgt ggtaatactc
     6001 cggtattacc ttttatttct ttattttcat gtaattacag tggattttta atacccgggt
     6061 attactcgtg aaaacgaaat attccttttt tttcttttaa ttcatgcagt tgcgatgaaa
     6121 atcgcggctg cgttaggtgt atgaccattt tgaggttgaa aaataatcaa ccatggcggg
     6181 tgatttacgc aggttaaggg gagatcgtga c
//
