LOCUS       NZ_CP053240             5689 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-106 plasmid pSCU-106-6, complete
            sequence.
ACCESSION   NZ_CP053240
VERSION     NZ_CP053240.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609771
            Assembly: GCF_013085185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5689)
  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  JOURNAL   Unpublished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 5689)
  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                   :: 14x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:10:47
            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)                     :: 5,452
            CDSs (total)                      :: 5,328
            Genes (coding)                    :: 5,059
            CDSs (with protein)               :: 5,059
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 0 of 269
            Pseudo Genes (frameshifted)       :: 108 of 269
            Pseudo Genes (incomplete)         :: 154 of 269
            Pseudo Genes (internal stop)      :: 52 of 269
            Pseudo Genes (multiple problems)  :: 47 of 269
            Pseudo Genes (short protein)      :: 3 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053240.1.
            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..5689
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-106"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-106-6"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(<1..436)
                     /locus_tag="HHJ24_RS26860"
                     /old_locus_tag="HHJ24_26855"
     CDS             complement(<1..436)
                     /locus_tag="HHJ24_RS26860"
                     /old_locus_tag="HHJ24_26855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522465.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="WP_170969618.1"
                     /translation="MEYSTLLSFAIVTLSQTISIGPGVALVINNAFSHGLKSSIKTSIY
                     IRIGETIVMAISLFALSSTSSTEQHFHIIKIFGGGYLIYIGLMGLINKKNKQRKEQKPF
                     LIPLLNPKAYLFFAALIPTFIDNNTNITLNFFILGVLFIFI"
                     /name="LysE family translocator"
     gene            complement(443..1393)
                     /locus_tag="HHJ24_RS26865"
                     /old_locus_tag="HHJ24_26860"
     CDS             complement(443..1393)
                     /locus_tag="HHJ24_RS26865"
                     /old_locus_tag="HHJ24_26860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001058673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_137488420.1"
                     /translation="MNNFINECISAPRINGMAEFFSSTASGEKHKPFRLVEIDDRLFHS
                     YDYIKFAKHLTKNSGPFVNHYFCSIPYSKEEECRLGTTVIKYAITLNKKLNTWCLGMAE
                     GAMARTISELSKGNIQTLTTSPTKENEHAFFKYGSSENAYFICSPFFLLEERLKNSNLK
                     QFNQGFDIIIEDTTFQMYSPNRSGQINHVKRLLNNDGIFIFTEKHSSEHDEYQKREIQK
                     DYSFKQRYFSKDEINTKKEIVLNTMNLNEVSVDDMLSAIKQHFKYASIYWNSGNFYSIA
                     ASNSLKHISTFINLLPKAAIPMEYVYEKLPRNISW"
                     /name="hypothetical protein"
     gene            1946..2851
                     /locus_tag="HHJ24_RS26870"
                     /old_locus_tag="HHJ24_26865"
     CDS             1946..2851
                     /locus_tag="HHJ24_RS26870"
                     /old_locus_tag="HHJ24_26865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237866.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_015058918.1"
                     /translation="MSAVLQRFREKLPHKPYCTNDFTYGVRILPKDIAILARFIQQNQP
                     HAQHWLVFDVDRTGAAIDWSDRNCPAPNITVKNPRNGHAHLLYALTLPVRTAPDASASA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHQEWQVVEWRLELYTLDELADYLDLSASA
                     RRRVDKDYGMGRNWYLFEKSRKWSYRAIRQGWPAFSQWLDAVIQRVEMYNASLLVPLSP
                     AECRAIGKSIAKYTYRKFSPEGFSAVQAARGRKGGKIGGAKSKRVAVPTSARSLKPWEA
                     LGISRATYYRKLKCDPDLAK"
                     /name="replication initiation protein"
     gene            complement(3056..3502)
                     /locus_tag="HHJ24_RS26875"
                     /old_locus_tag="HHJ24_26870"
     CDS             complement(3056..3502)
                     /locus_tag="HHJ24_RS26875"
                     /old_locus_tag="HHJ24_26870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_016230928.1"
                     /translation="MTNLEEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAILAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFNAAELVGALAGVAELPRNHPKWQEWEKRGKELLTKDGA"
                     /name="conjugal transfer protein TraD"
     gene            3673..4758
                     /locus_tag="HHJ24_RS26880"
                     /old_locus_tag="HHJ24_26875"
     CDS             3673..4758
                     /locus_tag="HHJ24_RS26880"
                     /old_locus_tag="HHJ24_26875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001530418.1"
                     /translation="MASYHCTVKTGAKGVALKHADYISRSGEYKNYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKARF
                     GETPQERKSALVALRSHWADVQNEHLARHGHQSRVDHRSLKEQGIKRTPEVHLGPVRVA
                     VMNADQVCAILARRNAEREKLEAEQERDSIIDLKTTLKEALAERDNIPPSLDELGAELK
                     AFVESSFDELNEVMQLNSLINGALDSMMKQFQVEEERKLQQERLIEAEKQRDLERERER
                     VRQRAYSSPAPSRSRDYGMSR"
                     /name="MobA/MobL family protein"
     gene            4779..5495
                     /locus_tag="HHJ24_RS26885"
                     /old_locus_tag="HHJ24_26880"
     CDS             4779..5495
                     /locus_tag="HHJ24_RS26885"
                     /old_locus_tag="HHJ24_26880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235968.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001175444.1"
                     /translation="MQLDEHSRKIAALVAYNDKQIKEMNRLITLLNERVNDLNTFTSTL
                     EREGKVVSGISYSFRDSVSNVKFYINKGMDEASCKLQKSVSDTLTSLLREKLSFTLNDV
                     KKEWVDFEEQTSKEIKESLKQTTREAEVATGIIRKTMEKYTVTRIVEKVIVLIVLFLLL
                     MIAPVFYAEYLKMNISSLMEEQKKHESMLKEWKEKAPLAEFSKCGDYRKACVLVDDESG
                     YYFNEQSPNKKYAILK"
                     /name="hypothetical protein"
     Typing          1947..2851
                     /name="rep_cluster_2141"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.89"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3674..4755
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atataaatat aaataaaaca cccaatataa aaaagtttaa tgtgatattt gtattattat
       61 ctataaaggt tggtattaac gcagcaaaga aaagatacgc cttggggttt aataatggta
      121 tcaaaaaagg tttttgctct tttctttgtt tgtttttttt attaattaaa cccattaatc
      181 ctatgtatat taaatagcct ccaccgaata tttttataat gtgaaaatgt tgttctgtgc
      241 tggatgttga ggataacgcg aaaagagata ttgccatgac gatagtctcg ccaattctta
      301 tgtatatact tgtttttatt gatgacttta atccatgtga aaaggcattg tttataacca
      361 atgcaacgcc aggccctatt gatatagttt gcgataaggt tacgatagca aatgataata
      421 atgttgaata ttccatgttt acttaccatg atatatttcg tgggagcttt tcatatacat
      481 attccatagg aattgcagct ttcggtaata aatttataaa tgttgatatg tgttttagtg
      541 aattgctggc ggcgattgag taaaaatttc cgctattcca atatattgat gcgtatttaa
      601 aatgttgttt aattgcggaa agcatatcgt caacactaac ttcattcaaa ttcattgtgt
      661 ttagtacgat ttcctttttg gtgttaatct catctttcga gaaatacctt tgtttgaatg
      721 aataatcttt ttggatttct cttttttgat attcatcatg ttctgaacta tgtttttctg
      781 taaatatgaa aataccatca ttatttaata gcctttttac gtggtttatt tgcccagatc
      841 tgttaggtga gtacatttga aatgtggtgt cttctattat aatatcgaat ccttgattaa
      901 attgtttaag atttgaattt tttagtcttt cctctaacag gaaaaatgga ctgcaaataa
      961 aataagcgtt ttcacttgag ccatacttaa aaaatgcatg ttcattttct tttgttggac
     1021 tggttgttaa tgtttgtatg tttccttttg ataattctga aatggttctt gccattgcgc
     1081 cctcagccat accaagacac catgtgttta attttttgtt tagcgtgatt gcgtatttta
     1141 ttactgttgt tcctaatctg cactcttctt ccttgctgta tggtatactg caaaaataat
     1201 gattaacgaa agggccgctg ttttttgtga ggtgtttggc aaacttaatg taatcataag
     1261 aatgaaaaag ccgatcatct atttctacta gtctaaaagg tttgtgtttt tcccctgatg
     1321 cagttgatga gaaaaattct gccatgccgt ttattctcgg agcggaaata cattcattta
     1381 taaaattatt cattttccta tcctctggtt tgatttttgg aatttgttgt tatgactctt
     1441 caatgctaat tctcttgtaa gcttttttac acgccataaa cacgattatg atgttttata
     1501 ttgtcgatat ttcgttgtcc agactggata tgtttggaaa tttgttttca tgcgggttag
     1561 ttcagctggc tttctggatg agaaagtttg ctgttttgac cagttcgcgc ttctgaaggg
     1621 gtgaaaccga tcattaatcg cttttgtgca tagttatgca ggcccctaaa aacgattctg
     1681 acgcgttttt tgtgttttcc ctaggtttat cttgtctttt tgagtttttt gcgtcagaaa
     1741 gcgattgaga gcgttttaga gggtacgtac aaggggagtt atggtaaatg gatcgggttt
     1801 tcgtgatgga tcgacagggt ttgtcgttgg gtgtagtgta agcagctgaa aaacaaacgc
     1861 ccctgaaatt cgtgccgatc cgccaagact gtcacgaaaa ttcaaggggc gtgtgggttg
     1921 taacacacag aggaaatcct aacacatgag cgccgtactt caacgcttca gggaaaaatt
     1981 accgcacaaa ccgtactgta cgaacgattt cacgtacggc gttcgcattc tgccgaaaga
     2041 tatcgccatc cttgcccgtt tcatccagca gaaccagcca catgcgcagc actggcttgt
     2101 ttttgacgtg gaccggacgg gcgcagcgat agactggagc gaccggaact gtccggcccc
     2161 gaatatcacc gtaaaaaatc cccgtaacgg gcacgcgcat ctgctttacg cactcactct
     2221 tccggtgaga accgcgccgg atgcatcggc ttcggcgctc aaatacgctg ctgcgattga
     2281 gcgtgcactg tgtgaaaaat taggcgcgga tgtgaactac agcggcctga tctgcaaaaa
     2341 tccgttccat caggaatggc aggttgtgga atggcgtctg gaactctata ccctcgatga
     2401 actggcggat tatctcgatt tgagcgcctc agcgcgccgt cgcgtcgata aagattacgg
     2461 gatggggcga aactggtatc tgttcgaaaa gagccgtaaa tggtcttaca gggcgattcg
     2521 tcagggttgg ccagcattct cacagtggct tgatgccgtg attcagcgtg tcgaaatgta
     2581 caacgcatcg cttctcgttc cgctttcacc ggctgaatgt cgggctattg gcaagagtat
     2641 tgctaaatac acctaccgaa aattctctcc tgaaggtttt tctgcggtac aggctgcgcg
     2701 tggtcgcaaa ggtggaaaaa taggcggtgc taaatccaag cgtgtagcag ttcctacatc
     2761 agcgcgttct ctgaagccgt gggaggcatt agggatcagt cgagctacgt actaccgaaa
     2821 attaaaatgt gatccagatc tcgcaaaatg agaccagata aagccttatc agataacagc
     2881 gctccgttgg cgtttttttg agctgttggt tttgctgtgt atttctctgc tcacccccgc
     2941 aatggtgcgg ctttccgcat gattgaggtg gtagtgctcg ccgcagtctc atgaccgagc
     3001 gtagcgagcg aatgagcgag gaagcaccag ggtaccagaa cgcgaacgga gactcttacg
     3061 caccgtcttt ggtgagtagc tctttcccgc gtttttccca ttcctgccat tttggatggt
     3121 tgcgtggtag ctctgctact cctgctagtg cgcctaccag ttcggcagca ttaaattttg
     3181 gttttccggt tttgctgtcc actagtccag caacaatcat gaggcctgcg gctttgtaga
     3241 gttcgtgatc ccgcgccttt cgttctgccc ttgcggcagc cttccgttct gccgcaagga
     3301 ttgctgttac cctagctttt gcagcggcgg ctttctccgc ggttttttct gctcgtatta
     3361 gtgcggataa cgttttttca tccgtcgttg ttcggttttt tttctctgcc agtaatacaa
     3421 gtaatcgctg ctgctcagat ggtgatttca gaccgttgat gtaggcaatt tttgcactta
     3481 accactcttc aagatttgtc attcttatct ccgcactttt gccgtttatt gttttggtat
     3541 tgcgcataat atcaccttgt atgcccgagt acgtgaccgt aaaatcatcc ctgataaact
     3601 tagggatgcg cacttagacg tttctctcct tcgtcgagaa acagtgcgct cctgcggagg
     3661 gcttaacggc agatggcaag ctaccattgt acagttaaaa ctggagcaaa aggcgtagcc
     3721 ttaaaacatg ctgattatat ttctagatcc ggcgaatata agaactacaa atcgcgggag
     3781 gatctggaat tttcgtcatc cggtaacatg ccatcatggg cgaagaaaaa tcccgcagag
     3841 ctatggaaag cagcagatga atttgaacga aaaaacggga cggcataccg tgaaattgag
     3901 atcgcattac cgcgagaact gacacgcgaa caacggatag aacttgttga agatttcgtg
     3961 caaaaggagc ttggtgatcg ccatgcctat cagtacgcga tccacaatcc gccaggtgca
     4021 atcgacggaa aggaacaacc acacgcacat atcatgtttt gcgagcggat taatgatggt
     4081 attgaacgcg atccgcagca gttttttaaa cgtgccaaca gcaaatcacc ggagcgggga
     4141 ggtgcaaaaa aggcacgctt tggtgagaca ccacaagagc gaaaatcagc cttggttgcg
     4201 ctacgttctc actgggctga tgtgcagaat gaacaccttg cgcggcacgg ccatcagtcg
     4261 cgcgttgatc atcgttcact gaaagaacag ggtatcaagc gcacaccgga agttcatctt
     4321 ggtcccgttc gtgttgctgt tatgaatgct gatcaggttt gtgcaattct ggcacggaga
     4381 aacgcggaac gggagaagct agaagcagag caggaacggg acagcatcat tgaccttaaa
     4441 acgaccttga aggaagcgtt agctgaacgg gataacatac caccaagcct ggatgagctt
     4501 ggggcagaat tgaaggcgtt tgttgaaagc tcgtttgatg aactcaatga ggtaatgcag
     4561 cttaattcat tgattaacgg tgcgctggac tcaatgatga agcaattcca ggtggaagag
     4621 gagcggaagt tgcaacagga acgactaatt gaagccgaaa agcaaagaga cctggagagg
     4681 gaaagagaaa gagtgcgcca gcgtgcgtat tcctcaccag caccatcacg ttcacgtgat
     4741 tatggtatga gccgttaagc actggaggtt tttattttat gcaattggat gaacattcaa
     4801 gaaaaattgc tgctcttgtt gcgtataatg ataaacaaat aaaagaaatg aacaggctaa
     4861 ttactctgct taatgaaaga gtgaatgact taaatacctt tacaagtact cttgaacgtg
     4921 aaggtaaagt tgtttctgga atttcttatt cctttaggga tagtgtgtct aatgttaaat
     4981 tttatattaa taaaggaatg gatgaggcat cttgtaaatt acagaaatca gtctcagata
     5041 cactaacgtc attactccgc gaaaaattat ctttcactct caatgatgta aagaaagagt
     5101 gggttgattt cgaggagcaa acaagtaaag agataaagga atcattaaag cagacgacca
     5161 gagaggccga agttgcgaca ggtataatta gaaaaacaat ggagaagtat acagtaacaa
     5221 ggattgtcga aaaggtaatt gtgttgattg tattattttt attgctaatg atcgctcctg
     5281 ttttctatgc tgaatatctc aaaatgaata ttagttcgct aatggaagaa cagaaaaaac
     5341 atgaatccat gttaaaagaa tggaaagaaa aagctccatt ggccgagttc tcgaagtgtg
     5401 gagattatcg taaagcatgc gtgttagttg atgacgaaag cggatattat tttaatgaac
     5461 aatcaccaaa taaaaaatat gccatactga aatagtgtta agtaactcat gccgtcttat
     5521 gactaaggct gcatgagtat aaaaacggcg tttcacgtaa aaataaaata aatacctgta
     5581 cctaatataa aaatggaact acatatgctt atgtatcttg agaatgatgg cgtcaattta
     5641 tcccttatcg ttaagctaat agctatgtaa ataagatctg ttaggaatg
//
