LOCUS       NZ_CP053249             5168 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-482 plasmid pSCU-482-2, complete
            sequence.
ACCESSION   NZ_CP053249
VERSION     NZ_CP053249.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609798
            Assembly: GCF_013085025.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5168)
  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  JOURNAL   Unpublished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 5168)
  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                   :: 34x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:02:06
            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)                     :: 5,216
            CDSs (total)                      :: 5,099
            Genes (coding)                    :: 4,789
            CDSs (with protein)               :: 4,789
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 310
            CDSs (without protein)            :: 310
            Pseudo Genes (ambiguous residues) :: 0 of 310
            Pseudo Genes (frameshifted)       :: 188 of 310
            Pseudo Genes (incomplete)         :: 139 of 310
            Pseudo Genes (internal stop)      :: 43 of 310
            Pseudo Genes (multiple problems)  :: 58 of 310
            Pseudo Genes (short protein)      :: 4 of 310
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053249.1.
            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..5168
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-482"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-482-2"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            604..813
                     /locus_tag="HHJ51_RS25755"
                     /old_locus_tag="HHJ51_25755"
     CDS             604..813
                     /locus_tag="HHJ51_RS25755"
                     /old_locus_tag="HHJ51_25755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(879..1412)
                     /locus_tag="HHJ51_RS25760"
                     /old_locus_tag="HHJ51_25760"
     CDS             complement(879..1412)
                     /locus_tag="HHJ51_RS25760"
                     /old_locus_tag="HHJ51_25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(1415..2341)
                     /locus_tag="HHJ51_RS25765"
                     /old_locus_tag="HHJ51_25765"
     CDS             complement(1415..2341)
                     /locus_tag="HHJ51_RS25765"
                     /old_locus_tag="HHJ51_25765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2518..2916
                     /locus_tag="HHJ51_RS25770"
                     /old_locus_tag="HHJ51_25770"
     CDS             2518..2916
                     /locus_tag="HHJ51_RS25770"
                     /old_locus_tag="HHJ51_25770"
                     /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="hypothetical protein"
                     /protein_id="WP_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(3120..4034)
                     /locus_tag="HHJ51_RS25775"
                     /old_locus_tag="HHJ51_25775"
     CDS             complement(3120..4034)
                     /locus_tag="HHJ51_RS25775"
                     /old_locus_tag="HHJ51_25775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     Typing          complement(3260..4034)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(1419..2341)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acttaaagat tagcacacca cacaaaaaca ataaaaaaaa acgacaagtt atacaataaa
       61 accagtacta tccatacagc taattacata taaatactat taaaccatct ggacattaaa
      121 aataaactct tataacataa aattaatgcg gttccggtac catatgtcag ggataatgtg
      181 caaatggagg tatcggaact gcatttcagt tcattattaa ttaatgacaa aaaaaaacct
      241 ctgcgagcgc agagggggta aggaatgttc ccggtcataa tatgtcgata gtgtttatat
      301 acatacagaa caagaacaac aaccagccaa ctaataaata ttttattttt tagagctgaa
      361 accttaaagc tcacttccat tccatacatt gttataaacc ttatgttgaa aactgaaagt
      421 aagtacggca gacttattaa gttgcgtgca gtcttttcac gttatacaaa caagaacacc
      481 tgcgaagtta tttctcctta catatccccc tatgccaacg ggggattttt tctggttcac
      541 taacgcataa ataatagtga caccctatca ttcacaaacc gtgataatat aaggattatc
      601 atcatggcaa aattaggtga aaacacccca catattatcg atgctactgt agattttatg
      661 gcatcaagcc aggcatttcg tgagtatctg aaaaaacttc cccctgataa cacaataccg
      721 ccagctctta ctgatgagca cgtaccgtta tatatacgaa ggctggaata ctatcgtctg
      781 ctttatcgac caaagcagac agaatcatat tgaaaaaaac ggtgaacggt tcgcgaaatc
      841 ctttcgcggg tcgtgaggcg ttggacaagc gaagcgcgtc agtttttccg gctcttcccc
      901 gtgacaggtt tctccaccag tttatcttcc agtgtcacaa ctttctgata caccgccgct
      961 gtggcgttgt agttcctgtc gagtattgtt ttcattcccc atccgagcac acagaacata
     1021 accagaaaag ccactgacac cccacccagc catttccagc tatacccttt aagggtgttg
     1081 tattcctgca cgatattgct gtgaattgtc gcaatatccc tgttcagggc atccgcgttt
     1141 gccttcatgt ttgcgactga ctcttccagc cgctgaaaat cctggctgat gcgctcacct
     1201 atcagtcctg ccacgtccag cttctgcacc tcatttctga cttcatccct gacctgtttt
     1261 gccacaccgt cagaaatatc ccgatatccg cgaagagttt cccttgccac agccagagaa
     1321 tcagcaacag ctttctgttg ctccattgcg gtatgttgca gatgctccac cgataacagg
     1381 agcgtgagta atttttcttc tgtgctggcc atgttcagaa tcccatagaa aatccacgtg
     1441 acggtgattt aacccgttca ggtgcagttc ggttctgtct gctcactctg tctctcatgt
     1501 caaagccatg ctcccgcgca acatcatgtt gcagccttct gaccagttca tgttgcttaa
     1561 ccggagtgtc cagccattcc ctgatgtcat gcccgaccgt tcgcgcctgt tcaagatggc
     1621 gggaatagtc cggttcagac cgtttttgca tgatgtcatg acgctgggca tcatcaagcc
     1681 gtccggcagc ttcaaaaccc agatgcactt cgggacgtcg ttcaatgccc tgttctttca
     1741 gcgtccggca gtcaatgaag cccctttcaa agccatgctt tctcatatgt tcgttgtgct
     1801 tcacctccca gcgttttcgc aattcccgca actgctcttt ttgctgagtg agagtcaggc
     1861 ttccggaatc ctttttcgca cctccccgct cgggatacct ggcgttatag cgccggaaat
     1921 actgttccgg tgtacgttca atgccatcat tcacacgctg actcatcatg atatgcgcat
     1981 gaggctgttc gccgccgtca atgctcgctt tcggattgtg aatggcaaaa ctccaggcgt
     2041 gccgttcgcc agcttcctga cgtacaaaat cctgcaccag ttcaaggcgc tgttccggtg
     2101 tcagttcacg gggtaatgca atttcaagtt ccctataggt cgaaccgttc gcacgttcaa
     2161 actggtcagc cgcctgccag aaatgggaag gattatccct ggcccattcc ggcatgtttc
     2221 cgtgtgcgga atattccaaa tcctgacggt cgcggtattt ctctttgcgc tcgatgtaat
     2281 cggcgtggtt tgcagcctgc cccttgccac caaatttaac gctgaggtga taggttgcca
     2341 cggtttcagc cctctgcagg agcgcactgt ttctcgacga aggagagaaa catataagtg
     2401 cgcttccttc taattttacg aattagcacg gaagataccc cctgcacccg ccgaccgcaa
     2461 gcgatatact gcacgaccac aacacaccgc aaaaaaacac cagggagcat cacgaacatg
     2521 cgcatcagca acatcgaatg gctgaagaaa cggatcggat tcatcaggaa gctcggagaa
     2581 cagaccgcac gacagagaca gattattgac ctgatcgaca acgaagccgg actcacagaa
     2641 caggaacgca aacttctcca cgtactggca acagcggaaa aaaacgactt acaggcacag
     2701 gagagcgaac gaaaacaggc ggtccaaaaa cgaatcgagg gaaaaaaaca acgacgggaa
     2761 cgcaatcacc ggctctttct cgcggctggg ctactgatcg aagcaggact ggtagacaca
     2821 aaaacaggcg agctatgcta taaaaaagac aggatattac aagcacttaa ggaacttaag
     2881 tacgatctgg agacatcccc aaacccagac gcgtaagtgc ctccatccgt gttccgattc
     2941 cctggtgctt cctcgctcat tcgctcgcta cgctcggtca tgagactgcg gcgagcacta
     3001 ccaccacaat cacgcggaaa gccgcgccat tgcagggctg aacggggaaa aacggcaaaa
     3061 aacctgctgc tcaaaaagac gccagaaagg cgctgttatc tgatataggc ttatttggtc
     3121 tactctacga gacctcgttt tttcagttgg taataccagg cgcgactgat ccctaatgcc
     3181 tcccacggtt tcagcgtgcg tgcagatgta gctactgtgc tgcgcttaga cttagaaccg
     3241 cccttgcgac cgcgtgcagc ctgaatttct ggcgtgtgcg tatcagccac atactgtgcg
     3301 aaagtttccg gcgtgaagtt cctgtgcgtg tatttcgcaa tgctcttgcc aatagcccga
     3361 cattcagcca gtgaaagcgg aacgggaagc gatgcattgt acatttcgac acgctggatc
     3421 accgcttcaa gccactgtga gaacgctggc cagccctgac gaatcgccct gtaagcccat
     3481 ttgcgcgtca tttcgaacag gtggcagttt cgccccatcc cgtaatgttt atcgatgcta
     3541 cgacgctctg aggcgctcaa atcgagataa tcagccagtt catcgagggt ataggcttcc
     3601 tcgcgccact ccatcaccag ccattccagg tggaacggat ttttgcaaat caggccgctg
     3661 tagttcacat ccgcacaaag tttctcacac agcgaacgtt caaccgctgc ggcatatttc
     3721 agcgccttaa ccgaggcatc aggcgcggtt ctcacggcga tgttgagtgc gtagagcagg
     3781 tgagcgtgtc cgttcacagg atttttaacg gtgatgttcg gcgcgggagc gttccggtcg
     3841 ctccagtcaa tcgcagcccc ctcgcggtca acgtcaaaaa ccagccagaa ctgcgcatga
     3901 ggctggttct gctgtatgta ccgcgcaaga agcgcacgcc ctttgccgga gatgcgaaga
     3961 ccaaaagcga gatcatccgt gtgataggga cgatggggta aattttcgtc gaagtattga
     4021 agcgcggcgc tcatgtgtta cgattctctc cgggttatgc gacctacacg ccctctgtat
     4081 ttcatgttga atcttgccgg atctggacat gatttcaggg gcgtttgttt ttcagtcgct
     4141 tacactacac ccaacggcaa atcctgtcga accttcccga aaacccgatc catttaccat
     4201 aactcccgtt gtacgccccc cttaaaacgc cctcagtcgc tttctggcgc aaaaaacgca
     4261 aaaagacaag aaaacaccag gccaaaccag aaaaacgcgt cagaatcgtt ttcagggcgt
     4321 tgcataacta tgcacgaaag cgatgtgcga tcggtttcgt gcgttctgaa caccgaacgg
     4381 ctcaaaacga caagttttct cccctggtgc gtggcgctct gacggggttt cctgtttcca
     4441 aacttcacat ctcgccagga caaaaaaaaa ccgacctggg gtcggtggca agaatcagag
     4501 tctatgggaa atattttagt tatcggatgc tcaatattca caaacgcaaa aaatgcctca
     4561 gtgatgccct aaaacaacct ttccagaagg agtccgcgct ttacgatgca cggaagagat
     4621 aaaaaacccc acaaaagtgg ggaaccaaga gaaacaacaa ttacaggttg ttggttgtgt
     4681 tcgaacaacg atgaagtagc tacgctaaat aataattacc gtacaggccc tacatattca
     4741 acactaaatt taagatcctg acgaaggatt tataaatgca cgaaaacaca tagacagaca
     4801 aattcactaa attcatacac aaaaacaagt gtagttttct aagtaaatta gattcgacaa
     4861 ccaattagtt tatccacatc gcattccact cttgctacac caatcacatt tcttgatatg
     4921 taatagcaga aaaaataaaa ccagacacca atagaccaaa aaacaaacat tcaacaagaa
     4981 acattttgaa caatatcaca aaactgtcac aaccatcatc agactattga aaaaaactgg
     5041 ttgctgtttt ataaaagcga ctgtaacaac ctccactcta tagttccatt agtttaaagt
     5101 gtcacacaaa ctgagcatcc atttgttttc cttacttttg cccctgtatt ccaaggggtt
     5161 tttttata
//
