LOCUS       NZ_CP053241             5237 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-106 plasmid pSCU-106-7, complete
            sequence.
ACCESSION   NZ_CP053241
VERSION     NZ_CP053241.1
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 5237)
  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  JOURNAL   Unpublished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 5237)
  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
            CP053241.1.
            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..5237
                     /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-106-7"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            <1..391
                     /locus_tag="HHJ24_RS26890"
                     /old_locus_tag="HHJ24_26885"
     CDS             <1..391
                     /locus_tag="HHJ24_RS26890"
                     /old_locus_tag="HHJ24_26885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001681717.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0006865 - amino acid transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="LysE family transporter"
                     /protein_id="WP_170969619.1"
                     /translation="SSTSSIEQHFYIIKILGGSYLIYIGVMGLINKKNKKSKVQKPLLI
                     PLLNPKAYLFFAALIPAFIDDNTNIALNFFILGVLFIFISFLTDIIYIAISLTIRDKLT
                     PSFSRYISICSSIFILGTGIYFILT"
                     /name="LysE family transporter"
     gene            complement(449..1165)
                     /locus_tag="HHJ24_RS26895"
                     /old_locus_tag="HHJ24_26890"
     CDS             complement(449..1165)
                     /locus_tag="HHJ24_RS26895"
                     /old_locus_tag="HHJ24_26890"
                     /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_170969620.1"
                     /translation="MQLDEHSRKIAALVAYNEKQIKEINRIITLLNERVNDLNTFTDTL
                     EREGKVVSGISYSLRDSMSHVDFYLNKGMEEVSCKLQKSVSDTLTSLLREKLSFTLNDV
                     RQEWTDFEEQTSKEIKESLKQTTRDAEVATGIIRKTMEKYTVTRIVEKVLVLLVLFLLL
                     MIAPSFYAEYLKMNIGSLMEEQKKHESMLKEWKEKAPLAEFSKCGEYRDVCVLVDDKSG
                     YYSNEQTPNKKYAILK"
                     /name="hypothetical protein"
     gene            complement(1187..2281)
                     /locus_tag="HHJ24_RS26900"
                     /old_locus_tag="HHJ24_26895"
     CDS             complement(1187..2281)
                     /locus_tag="HHJ24_RS26900"
                     /old_locus_tag="HHJ24_26895"
                     /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_000179381.1"
                     /translation="MASYHCTVKTGAKGVALKHADYISRSGEYKNYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKARF
                     GETQQERKSALVALRSHWADVQNEHLARHGHQSRVDHRSLKEQGIKRTPEVHLGPVRVA
                     VMNADQVCAILAWRNAEREKLEAEKERDSIIDLKTTLKEALAERDNMPPTLDELGAELK
                     AFVESSFDELNEVMQLNSLIDGALDTMMKQFQVEEERKLQQERLIQAARDEAEKQRELE
                     RERVRRRAYSSPAPSRSRDYGMSR"
                     /name="MobA/MobL family protein"
     gene            2453..2899
                     /locus_tag="HHJ24_RS26905"
                     /old_locus_tag="HHJ24_26900"
     CDS             2453..2899
                     /locus_tag="HHJ24_RS26905"
                     /old_locus_tag="HHJ24_26900"
                     /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_062864536.1"
                     /translation="MTNREDWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARVERKARDHELYKAAGLMIVARLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(3424..4455)
                     /locus_tag="HHJ24_RS26910"
                     /old_locus_tag="HHJ24_26905"
     CDS             complement(3424..4455)
                     /locus_tag="HHJ24_RS26910"
                     /old_locus_tag="HHJ24_26905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /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_062891489.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSEKQADKGRKG
                     GKNSGAVRWTANDDKRRRALDMYILGASTEDIAEAVGVSRWTVRRWMDSSVEWLLSKQI
                     IKF"
                     /name="replication initiation protein"
     Typing          complement(3680..4455)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.401"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(1191..2281)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.055"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcttcaaca tccagcatag aacaacactt ttacattata aagatcttag gtggaagcta
       61 tttaatatac ataggggtaa tgggtttaat taataaaaaa aacaaaaaaa gcaaagtaca
      121 aaaaccttta cttataccat tattaaaccc aaaggcgtat ttattctttg cggcattaat
      181 accagcattt atagatgata atacaaatat cgcattaaat ttctttatat tgggtgtttt
      241 gtttatattt atatcattcc tgacagatat tatttacata gctattagct tgacgataag
      301 ggataaatta actccgtcat tctcaaggta cataagtata tgtagctcca tttttatatt
      361 aggtacaggt atttatttta tcttgacgtg aaacgccgtt tttatactca tgcagcctta
      421 gtcataagac ggcatgagtt acttaacact atttcagtat ggcatatttt ttatttgggg
      481 tttgttcatt ggaataatat ccgcttttat catcaactaa cacgcatacg tccctatact
      541 ctccacactt agagaactct gccaatggtg ctttttcctt ccactctttt aacatagatt
      601 catgtttttt ctgttcttcc attagagaac cgatattcat tttgagatat tcagcataaa
      661 aactaggagc aatcattaac aataaaaata atacaagcaa cacaagtacc ttttcgacta
      721 tccttgttac tgtatacttc tccattgttt ttctaattat acctgtcgca acttcagcat
      781 ctctggtcgt ctgctttaat gattccttta tctctttact tgtttgctct tcaaaatcag
      841 tccactcttg ccttacatca ttaagtgtga aagataattt ttcacggagt aatgatgtta
      901 gtgtgtctga gacagatttc tgtaatttac aggatacttc ttccattcct ttattaagat
      961 aaaaatcaac atgagacata ctatccctca aggaataaga aattccagat acaactttac
     1021 cttcacgttc aagagtatct gtaaaggtat ttaagtcatt cactctttca ttaagcagag
     1081 taattatcct gtttatttct tttatttgct tttcattata cgcaacaagg gcagcaattt
     1141 ttcttgaatg ttcatccaat tgcataaaat aaaaaacctc cagtgcttaa cggctcatac
     1201 cataatcgcg tgaacgtgat ggtgctggtg aagaatacgc acgccggcgc actctttccc
     1261 tctccagctc tctttgcttt tcggcttcat ctcgcgcagc ctgaattagt cgttcctgtt
     1321 gcaacttccg ctcctcttcc acctggaatt gcttcatcat tgtgtccagc gcaccgtcaa
     1381 tcaatgaatt aagctgcatt acctcattga gttcatcaaa cgagctttca acaaacgctt
     1441 tcaattctgc cccaagctca tccagggttg gtggcatgtt atcccgttca gctaacgctt
     1501 ccttcaaggt cgttttaagg tcaatgatgc tgtcccgttc cttctcggcc tccagcttct
     1561 cccgttccgc atttctccat gccagaattg cacaaacctg atcagcgttc ataacagcaa
     1621 cacgaacggg accaagatgc acctccggcg tacgcttgat accctgttct ttcagcgaac
     1681 gatgatcaac gcgcgactgg tggccgtgtc gcgcaaggtg ttcattctgc acatcagccc
     1741 agtgagagcg tagcgcaacc agggctgatt ttcgctcttg ttgtgtctcg ccaaagcgtg
     1801 ctttttttgc gcccccccgc tctggtgatt tgctgttggc acgtttaaaa aactgctgcg
     1861 gatcgcgttc aataccatca ttaatccgtt cgcaaaacat gatatgcgcg tgtggctgtt
     1921 ccttcccgtc aattgcacct ggtggattgt ggatcgcgta ctgataggca tggcgatcac
     1981 caagttcctt ttgcacgaaa tcttcaacaa gctctatccg ttgttcacgt gtcagttctc
     2041 gcggtaatgc gatctcaatt tcacggtatg ccgtcccgtt ttttcgttca aattcatcag
     2101 cagctttcca cagttctgcg ggatttttct tcgcccatga tggcatgtta ccggatgaag
     2161 aaaattccag atcctcccgc gatttatagt ttttatattc gccggatctg gaaatgtaat
     2221 cagcatgttt taaggctacg ccttttgctc cagttttaac tgtgcaatgg tagcttgcca
     2281 tctgccgtta agccctccgc aggagcgcac tgtttctcga caaaggagag aaacgtctaa
     2341 gtgcgcatcc ctgaattaat cagggatgat tttacggtct cacacgcagg cagacaaggt
     2401 gatattatgc acaataacaa ctcacattaa cggcaaaagt gcagaggtaa ggatgacaaa
     2461 tcgtgaagac tggttaagtg caaaaattgc ctacatcaac ggactgaaat caccgtcaga
     2521 gcagcagaga ttacttgtgt tactggcaga gaaaaaaaac cgaacaacga cggatgaaaa
     2581 aacgttgtcc gcactgatac gggcagaaaa aaccgcagag aaagcagccg cagcaaaagc
     2641 cagagtaacg gcaatcatag cggcagaacg gaaggcagcc gcaagggtgg aacgaaaggc
     2701 acgagatcat gaactctaca aggccgcagg cctcatgatt gtggcacgac tggtggacag
     2761 caaaaccgga aaaccaaagt ttagtgctgc cgaactggta ggcgcactcg caggaatcgc
     2821 agagctaccg cgcaaccatc caaaatggca ggaatgggaa aaacgcggga aagagctact
     2881 caccaaagac agtgcgtaag agcctccgtt cacgttccgg ttccctggtg cttcctcgct
     2941 cattcgctcg ctacgctcgg tcatgagact gcggcgagca cgaccacctc aatcataccg
     3001 taagccgcac cattgctggg ctgaaagaag aaaaccgccg gaaagcccgc tgctcaaaaa
     3061 aacgccgaaa aggcgctgtt atctgatata ggctatttgt gcattgccca atttcgcgac
     3121 gcgcatacgc acggggggat ctggtgcgta agtgcctgat gtaactcctg tagatcttcc
     3181 gcttcctcgc ccactcgcga gcctggcggc tcggtcgcta gggctgcggc gagcggagcc
     3241 gccactcgct tggtttgcag ggtttcggta tttggtttgg gggtgtggga gcgggtcgga
     3301 gacaccgcgc aaaaaaacac caaacccccg ttcgggcgct gttatctgat ataggcttgc
     3361 ttcgtgcacc caaaattaac aaaaaaataa caaaataggg gggtgatgtg ttctttttgt
     3421 taattaaaat ttaattattt gtttactcag tagccattct acagagctat ccatccagcg
     3481 tcgaacagtc caacggctaa caccaaccgc ctctgcaata tcttctgttg aggctcccaa
     3541 gatgtacata tcaagcgccc tacgacgttt gtcgtcgtta gcagtccacc gaacagcgcc
     3601 actgtttttg ccgcccttgc ggcccttgtc ggcctgtttt tccgacgaat tggccttacc
     3661 gcccttgcga cctcgtgcgg cctgaatttc tggcgtgtgc gtatcagcca catactgtgc
     3721 gaaagtttct ggcgtgaagt tcctgtgcgt gtatttcgca atgctcttgc caatagcccg
     3781 acattcaggc ggtgaaagcg gaacgggaag cgatgcgttg tacatttcga cacgctgaat
     3841 cacagcatca agccactgtg agaatgctgg ccagccctga cgaatcgccc tgtaagccca
     3901 tttgcgcgtc atttcgaaca gatggcagtt tcgccccatc ccgtaatgtt tatcgatgct
     3961 acggcgcgct gaggcgctca aatcgagata atcagccagt tcatcgaggg tataggcttc
     4021 ctcgcgccac tccatcacct gccattccag gtggaacgga tttttgcaaa tcagtccgct
     4081 gtagttcaca tctgcacaaa gtttctcaca cagcgaacgt tcaatcgcag cggcgtattt
     4141 cagcgcctta accgagctgt ccggcgcggt tctcacggcg atattgagcg cgtagagcag
     4201 gtgagcatga ccgttcacag gattttttac ggtgatgttc ggcgcgggag cgttccggtc
     4261 gctccagtca atcgctgccc cctcgcggtc aacgtcaaaa accagccaga actgcgcatg
     4321 aggctggttc tgctgtatgt accgcgcaag aagcgcgcgc cctttgccgg agatgcgaag
     4381 accaaaagcg agatcatccg tgtgataggg acggtgcggt aaattttcgt cgaagtattg
     4441 aagcgcggcg ctcatgtgtt acgattctct ccgggttatg cgacctacac gccctctgta
     4501 tttcatgttg aatcttgccg gatctggaca tgatttcagg ggcgtttgtt tttcagtcgc
     4561 ttacactaca cccaacggca aatcctgtcg atccttcccg aaaaactgat ccatttacca
     4621 taactcctgt tgtacgtacc ctctaaaacg ctctcaatcg ctttctgacg caaaaaacgc
     4681 aaaaagacaa gaaaacacta gggtaaacca taaaaacgcg tcagaatcgt ttttatgggc
     4741 ctgcataact atgcacaaaa gcgattcatg atcggtttcc ccccttcaga agcgcgaacg
     4801 ggtcaaaaca gcaaactttc tcatccaaaa agccagctaa acggaacgaa cccgtatgca
     4861 aacaaatttc caaacatata cagtctggac aacgaaatat cgacaatata ttggaatagc
     4921 ggaaattttt actcaatcgc cgccagcaat tcactaaagc acatatccac atttataaat
     4981 ttattaccga aagccgcaat tcctatggaa tatgtatatg aaaagctccc acgaaatata
     5041 tcatggtaag taaatatgga atattcaaca ttattttcat ttgctatcgt aactttatct
     5101 caaactatat caataggacc tggtgttgca ttggttataa acaacgcctt ttcacaagga
     5161 cttaaatcat caataaaaac aagtatatac ataagagctg gcgaagcaat cgtcatggta
     5221 atatctcttt tcacgtt
//
