LOCUS       NZ_CP054357             5716 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-172 plasmid pSCU-172-4, complete
            sequence.
ACCESSION   NZ_CP054357
VERSION     NZ_CP054357.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943545
            Assembly: GCF_013315695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5716)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Title: F plasmids are the major carriers of antibiotic resistance
            genes in human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5716)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-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                   :: 78x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:55:40
            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)                     :: 5,461
            CDSs (total)                      :: 5,339
            Genes (coding)                    :: 5,056
            CDSs (with protein)               :: 5,056
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 85 of 283
            Pseudo Genes (incomplete)         :: 198 of 283
            Pseudo Genes (internal stop)      :: 39 of 283
            Pseudo Genes (multiple problems)  :: 33 of 283
            Pseudo Genes (short protein)      :: 3 of 283
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054357.1.
            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..5716
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-172"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-172-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            join(5567..5716,1..423)
                     /locus_tag="HPE50_RS26860"
                     /old_locus_tag="HPE50_26860"
     CDS             join(5567..5716,1..423)
                     /locus_tag="HPE50_RS26860"
                     /old_locus_tag="HPE50_26860"
                     /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_000456846.1"
                     /translation="MEYSTLLSFAIVTLSQTISIGPGVALVINNAFSHGLKSSIKTSIY
                     IRIGETIVMAISLFALSSTSSTEQHFHIIKIFGGGYLIYIGLMGLINKKNKQRKEQKPF
                     LIPLLNPKAYLFFAALIPTFIDNNTNITLNFFILGVLFIFISFLTDLIYIAISLTIRDK
                     LTPSFSRYISICSSIFILGTGIYFIFT"
                     /name="LysE family translocator"
     gene            complement(481..1197)
                     /locus_tag="HPE50_RS26865"
                     /old_locus_tag="HPE50_26865"
     CDS             complement(481..1197)
                     /locus_tag="HPE50_RS26865"
                     /old_locus_tag="HPE50_26865"
                     /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"
     gene            complement(1218..2303)
                     /locus_tag="HPE50_RS26870"
                     /old_locus_tag="HPE50_26870"
     CDS             complement(1218..2303)
                     /locus_tag="HPE50_RS26870"
                     /old_locus_tag="HPE50_26870"
                     /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            2475..2921
                     /locus_tag="HPE50_RS26875"
                     /old_locus_tag="HPE50_26875"
     CDS             2475..2921
                     /locus_tag="HPE50_RS26875"
                     /old_locus_tag="HPE50_26875"
                     /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_000184722.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(3128..4057)
                     /locus_tag="HPE50_RS26880"
                     /old_locus_tag="HPE50_26880"
     CDS             complement(3128..4057)
                     /locus_tag="HPE50_RS26880"
                     /old_locus_tag="HPE50_26880"
                     /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_032195366.1"
                     /translation="MSAVLQLFREKLPHKPYCTNDFTYGVRILPKDIAILARFIQQNQP
                     HAQHWLAFDVDRTGAAIDWSDRNCPAPNITVKNPRNGHAHLLYALTLPVRTAPDASASA
                     LKYAAVIERALCEKLGADVNYSGLICKNPFHQEWQVVEWRWELYTLDELADYLDLSASA
                     RRRVDKDYGMGRNWYLFEKGRKWSYRAIRQGWPAFSPWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTYRKFSPEGFSAVQAARGRKGGNANSSENQAIKGQKSKRVAVATSA
                     RTLKPWVTLGISRATYYRKLKCDPDLAK"
                     /name="replication initiation protein"
     gene            4610..5560
                     /locus_tag="HPE50_RS26885"
                     /old_locus_tag="HPE50_26885"
     CDS             4610..5560
                     /locus_tag="HPE50_RS26885"
                     /old_locus_tag="HPE50_26885"
                     /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_062861064.1"
                     /translation="MNNFINECISAPRINGMAEFFSSTASGEKHKPFRLVEIDDRLFHS
                     YDYIKFAKHLTKNSGPFVNHYFCSIPYSKEEECRLGTTVIKYAITLNKKLNTWCLGMAE
                     GAMARTISELSKGNIQTLTTSPTKENEHAFFKYSSSENAYFICTPFFLLEERLKNSNLK
                     QFNQGFDIIIEDTTFQMYSPNRSGQINHVKRLLNNDGIFIFTEKHSSEHDEYQKREIQK
                     DYSFKQRYFSKDEINTKKEIVLNTMNLNEVSVDDMLSAIKQHFKYASIYWNSGNFYSIA
                     ASNSLKHISTFINLLPKAAIPMEYVYEKLPRNISW"
                     /name="hypothetical protein"
     Typing          complement(3129..4057)
                     /name="rep_cluster_2141"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.505"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1222..2303)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actatcgtca tggcaatatc tcttttcgcg ttatcctcaa catccagcac agaacaacat
       61 tttcacatta taaaaatatt cggtggaggc tatttaatat acataggatt aatgggttta
      121 attaataaaa aaaacaaaca aagaaaagag caaaaacctt ttttgatacc attattaaac
      181 cccaaggcgt atcttttctt tgctgcgtta ataccaacct ttatagataa taatacaaat
      241 atcacattaa acttttttat attgggtgtt ttatttatat ttatatcatt cctaacagat
      301 cttatttaca tagctattag cttaacgata agggataaat tgacgccatc attctcaaga
      361 tacataagca tatgtagttc catttttata ttaggtacag gtatttattt tatttttacg
      421 tgaaacgccg tttttatact catgcagcct tagtcataag acggcatgag ttacttaaca
      481 ctatttcagt atggcatatt ttttatttgg tgattgttca ttaaaataat atccgctttc
      541 gtcatcaact aacacgcatg ctttacgata atctccacac ttcgagaact cggccaatgg
      601 agctttttct ttccattctt ttaacatgga ttcatgtttt ttctgttctt ccattagcga
      661 actaatattc attttgagat attcagcata gaaaacagga gcgatcatta gcaataaaaa
      721 taatacaatc aacacaatta ccttttcgac aatccttgtt actgtatact tctccattgt
      781 ttttctaatt atacctgtcg caacttcggc ctctctggtc gtctgcttta atgattcctt
      841 tatctcttta cttgtttgct cctcgaaatc aacccactct ttctttacat cattgagagt
      901 gaaagataat ttttcgcgga gtaatgacgt tagtgtatct gagactgatt tctgtaattt
      961 acaagatgcc tcatccattc ctttattaat ataaaattta acattagaca cactatccct
     1021 aaaggaataa gaaattccag aaacaacttt accttcacgt tcaagagtac ttgtaaaggt
     1081 atttaagtca ttcactcttt cattaagcag agtaattagc ctgttcattt cttttatttg
     1141 tttatcatta tacgcaacaa gagcagcaat ttttcttgaa tgttcatcca attgcataaa
     1201 ataaaaacct ccagtgctta acggctcata ccataatcac gtgaacgtga tggtgctggt
     1261 gaggaatacg cacgctggcg cactctttct ctttccctct ccaggtctct ttgcttttcg
     1321 gcttcaatta gtcgttcctg ttgcaacttc cgctcctctt ccacctggaa ttgcttcatc
     1381 attgagtcca gcgcaccgtt aatcaatgaa ttaagctgca ttacctcatt gagttcatca
     1441 aacgagcttt caacaaacgc cttcaattct gccccaagct catccaggct tggtggtatg
     1501 ttatcccgtt cagctaacgc ttccttcaag gtcgttttaa ggtcaatgat gctgtcccgt
     1561 tcctgctctg cttctagctt ctcccgttcc gcgtttctcc gtgccagaat tgcacaaacc
     1621 tgatcagcat tcataacagc aacacgaacg ggaccaagat gaacttccgg tgtgcgcttg
     1681 ataccctgtt ctttcagtga acgatgatca acgcgcgact gatggccgtg ccgcgcaagg
     1741 tgttcattct gcacatcagc ccagtgagaa cgtagcgcaa ccaaggctga ttttcgctct
     1801 tgtggtgtct caccaaagcg tgcctttttt gcacctcccc gctccggtga tttgctgttg
     1861 gcacgtttaa aaaactgctg cggatcgcgt tcaataccat cattaatccg ctcgcaaaac
     1921 atgatatgtg cgtgtggttg ttcctttccg tcgattgcac ctggcggatt gtggatcgcg
     1981 tactgatagg catggcgatc accaagctcc ttttgcacga aatcttcaac aagttctatc
     2041 cgttgttcgc gtgtcagttc tcgcggtaat gcgatctcaa tttcacggta tgccgtcccg
     2101 ttttttcgtt caaattcatc tgctgctttc catagctctg cgggattttt cttcgcccat
     2161 gatggcatgt taccggatga cgaaaattcc agatcctccc gcgatttgta gttcttatat
     2221 tcgccggatc tagaaatata atcagcatgt tttaaggcta cgccttttgc tccagtttta
     2281 actgtacaat ggtagcttgc catctgccgt taagccctcc gcaggagcgc actgtttctc
     2341 gacgaaggag agaaacgtct aagtgcgcat ccctgaatta atcagggatg attttaaggt
     2401 ctcacacgca ggcagacaag gtgatattat gcacaataac aactcacatt aacggcaaaa
     2461 gtgcagaggt aagaatgaca aatcgtgaag agtggttaag tgcaaaaatt gcctatatca
     2521 acggactgaa atcaccgtca gagcagcaaa gattacttgt gttactggca gagaaaaaaa
     2581 accgaacaac gacggatgaa aaaacgttgt ccgcactgat acgggcagaa aaaaccgcag
     2641 agaaagcagc cgcagcaaaa gccagggtaa cggcaataat agcggcagaa cggaaggcag
     2701 ccgcaagggc ggaacgaaag gcgcgggatc atgaactcta caaggccgca ggcctcatga
     2761 ttgtggcagg actggtggac agcaaaaccg gaaaaccaaa gtttagtgct gccgaactgg
     2821 taggcgcact cgcaggaatc gcagagctac cgcgcaacca tccaaaatgg caggaatggg
     2881 aaaaacgcgg gaaagagcta ctcaccaaag acagtgcgta agagcctccg ttcacgttcc
     2941 ggttccctgg tgcttcctcg ctcattcgct cgctacgctc ggtcattgag actgcggcga
     3001 gcacaaccac cactcacaca cagacgctaa aaccattgcc aaacgaaaca cgggaaatca
     3061 ccccaaacct acccgctcaa aaaaacgcct acaggcgctg ttatctgata aggcttgtta
     3121 tctggtctca ttttgcgaga tctggatcac attttagttt tcgatagtat gtggcacgac
     3181 tgatccctaa cgtcacccac ggcttcagag ttcgtgccga tgtggcaacg gctacacgct
     3241 ttgatttctg acctttaata gcctgatttt ctgatgaatt tgcattaccg cccttacgac
     3301 ctcgagcagc ctgtaccgcg gaaaagcctt caggagagaa tttgcggtag gtgtatttcg
     3361 caatactctt gccaatagcc cgacattcag ccggagaaag cggaacggga agcgatgcgt
     3421 tgtacatttc gacacgctga atcactgcat caagccacgg tgagaatgct ggccagccct
     3481 gacgaatcgc cctgtaagac catttacggc ccttttcgaa cagataccag tttcgcccca
     3541 tcccgtaatc tttatcgacg cgacggcgcg ctgaggcgct caaatcaaga taatccgcca
     3601 gttcgtcgag ggtatagagt tcccaacgcc attccaccac ctgccattcc tggtggaacg
     3661 gatttttgca gatcaggccg ctgtagttca catccgcgcc cagtttttca cacagcgcac
     3721 gctcaatcac ggcagcgtat ttgagcgccg aagccgatgc atccggcgcg gttctcaccg
     3781 gaagagtgag cgcgtagagc agatgcgcgt gcccgttacg tggatttttt acggtgatgt
     3841 tcggggccgg acagttccgg tcgctccagt cgatcgctgc ccccgtccgg tcaacgtcaa
     3901 aggccagcca gtgctgcgca tgtggctggt tctgctggat gaaacgggca aggatggcga
     3961 tatctttcgg tagaatgcga acgccgtacg tgaaatcgtt cgtacagtac ggtttgtgcg
     4021 gtaatttttc cctgaagagt tgaagtacgg cgctcatgtg ttaggatttc ctccgtgtgt
     4081 tacgacccac acgccccttg aattttcgtg acagtcttgg cggatcggca cgaatttcag
     4141 gggcgtttgt ttttcagttg gttacactac acccaacggc aaatcctgtc gatccttccc
     4201 gaaaaccaga cccatttacc ataactcctc ttgtacgtac cctctaaaac gctctcaatc
     4261 gctttctgac gcaaaaaact caaaaagaca agataaacct agggaaaaca caaaaaacgc
     4321 gtcagaatcg tttttagggg tctgcataac tatgcacaaa agcgattaat gatcggtttc
     4381 accccttcag aagcgcgaac tggtcaaaac agcaaacttt ctcatccaga aagccagctg
     4441 aactaacccg catgaaaaca aatttccaaa catatccagt ctggacaacg aaatatcgac
     4501 aatataaaac atcataatcg tgtttatggc gtgtaaaaaa gcttacaaga gaattagcat
     4561 tgaagagtca taacaacaaa ttccaaaaat caaaccagag gataggaaaa tgaataattt
     4621 tataaatgaa tgtatttccg ctccgagaat aaacggcatg gcagaatttt tctcatcaac
     4681 tgcatcaggg gaaaaacaca aaccttttag actagtagaa atagatgatc ggctttttca
     4741 ttcttatgat tacattaagt ttgccaaaca cctcacaaaa aacagcggcc ctttcgttaa
     4801 tcattatttt tgcagtatac catacagcaa ggaagaagag tgcagattag gaacaacagt
     4861 aataaaatac gcaatcacgc taaacaaaaa attaaacaca tggtgtcttg gtatggctga
     4921 gggcgcaatg gcaagaacca tttcagaatt atcaaaagga aacatacaaa cattaacaac
     4981 cagtccaaca aaagaaaatg aacatgcatt ttttaagtat agctcaagtg aaaacgctta
     5041 ttttatttgc actccatttt tcctgttaga ggaaagacta aaaaattcaa atcttaaaca
     5101 atttaatcaa ggattcgata ttataataga agacaccaca tttcaaatgt actcacctaa
     5161 cagatctggg caaataaacc acgtaaaaag gctattaaat aatgatggta ttttcatatt
     5221 tacagaaaaa catagttcag aacatgatga atatcaaaaa agagaaatcc aaaaagatta
     5281 ttcattcaaa caaaggtatt tctcgaaaga tgagattaac accaaaaagg aaatcgtact
     5341 aaacacaatg aatttgaatg aagttagtgt tgacgatatg ctttccgcaa ttaaacaaca
     5401 ttttaaatac gcatcaatat attggaatag cggaaatttt tactcaatcg ccgccagcaa
     5461 ttcactaaaa cacatatcaa catttataaa tttattaccg aaagctgcaa ttcctatgga
     5521 atatgtatat gaaaagctcc cacgaaatat atcatggtaa gtaaacatgg aatattcaac
     5581 attattatca tttgctatcg taaccttatc gcaaactata tcaatagggc ctggcgttgc
     5641 attggttata aacaatgcct tttcacatgg attaaagtca tcaataaaaa caagtatata
     5701 cataagaatt ggcgag
//
