LOCUS       NZ_CP054383             6237 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain SCU-175 plasmid pSCU-175-4, complete
            sequence.
ACCESSION   NZ_CP054383
VERSION     NZ_CP054383.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943546
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6237)
  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  JOURNAL   Unpublished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 6237)
  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                   :: 81x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:44:14
            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)                     :: 7
            CDSs (total)                      :: 7
            Genes (coding)                    :: 5
            CDSs (with protein)               :: 5
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 2
            CDSs (without protein)            :: 2
            Pseudo Genes (ambiguous residues) :: 0 of 2
            Pseudo Genes (frameshifted)       :: 1 of 2
            Pseudo Genes (incomplete)         :: 2 of 2
            Pseudo Genes (internal stop)      :: 0 of 2
            Pseudo Genes (multiple problems)  :: 1 of 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054383.1.
            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..6237
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-175"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-175-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(join(<6086..6237,1..202))
                     /locus_tag="HPE51_RS00005"
                     /old_locus_tag="HPE51_27640"
                     /pseudo=""
     CDS             complement(join(<6086..6237,1..202))
                     /locus_tag="HPE51_RS00005"
                     /old_locus_tag="HPE51_27640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557251.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(<726..845)
                     /locus_tag="HPE51_RS00050"
                     /pseudo=""
     CDS             complement(<726..845)
                     /locus_tag="HPE51_RS00050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001308260.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            877..1068
                     /locus_tag="HPE51_RS00015"
                     /old_locus_tag="HPE51_27650"
     CDS             877..1068
                     /locus_tag="HPE51_RS00015"
                     /old_locus_tag="HPE51_27650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165988.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDSENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2392..2619
                     /locus_tag="HPE51_RS00025"
                     /old_locus_tag="HPE51_27660"
     CDS             2392..2619
                     /locus_tag="HPE51_RS00025"
                     /old_locus_tag="HPE51_27660"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_015056439.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(2616..4181)
                     /locus_tag="HPE51_RS00030"
                     /old_locus_tag="HPE51_27665"
     CDS             complement(2616..4181)
                     /locus_tag="HPE51_RS00030"
                     /old_locus_tag="HPE51_27665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_042030235.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDKLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            4441..4878
                     /locus_tag="HPE51_RS00035"
                     /old_locus_tag="HPE51_27670"
     CDS             4441..4878
                     /locus_tag="HPE51_RS00035"
                     /old_locus_tag="HPE51_27670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001318234.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            4959..5378
                     /locus_tag="HPE51_RS00040"
                     /old_locus_tag="HPE51_27675"
     CDS             4959..5378
                     /locus_tag="HPE51_RS00040"
                     /old_locus_tag="HPE51_27675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     Typing          complement(1154..1241)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          1252..1810
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.606"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..244)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.531"
                     /coverage="81.0"
                     /evalue="8.860000000000001e-43"
     Typing          complement(6081..6235)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.154"
                     /coverage="81.0"
                     /evalue="1.31e-26"
ORIGIN
        1 tttcgagacc gggcatcagt acacgctcaa agctcgccat cacyttttca cgtcctcccg
       61 gyggcagctc cttctccgcg aacgacagma caccggacgt gtatttcttc gcaaatggcg
      121 tggcatcgat gagttcccgt acttcttccg gattaccctg aagcaccgtt gccccttccc
      181 ggttacgctc ccttcccagc aggtaatcaa ccggaccact gccaccacct ttccccccgt
      241 catgacagta acggcggttc ccgggtcggg agcccccccg gagggggaaa cggctcaccc
      301 cggcggaacc gccccctccc taccccccga tgttttccct caccgcggtg cagtaacccg
      361 gccggttcat catcagtaaa ccgtaacctg agcactctct tgcgttttgt ctgtatcact
      421 acccccccgc aaacaaaaac cccctacacg taggcagcag cggataaaaa ggaaaaaaac
      481 acccccaaca cagccccgcc ccccccctgc cccccrmcgc ccrccccacc cggccccccc
      541 cccccccgtg gsgcccccgg ggcgcccccc cccggacccg ggccgcsgga agccccctgc
      601 ccgctngtcc cccttccggg cttgtctggt tcggtttatc cccgakggct gccggcggcc
      661 gcagtaaccg gcggtgccgg tgccggcccc cccccggacc ggccacccgc cccccccagg
      721 cagccccgcc gcatccatac cgccagttgt ttaccctcac agcgttccag taaccgggca
      781 tgttcatcat cagtaacccg tatcgtgagc atcctctcgc gtttcatcgg tatcattacc
      841 cccatgaaca gaaatccccc ttacacggag gcatcagtga ctaaacagga aaaaaccgcc
      901 cttaacatgg cccgctttat cagaagccag acattaacgc tgctggagaa gctcaacgaa
      961 ctggacgcgg atgaacaggc agatatctgt gaatcgcttc acgaccacgc cgatgagctt
     1021 taccgcagct gcctcgcgcg cttcggggat gacagtgaaa acctctgaca tatacagctc
     1081 ccggagacgg tcacagcttg cctgtgagcg gatgccggga gcagacaagc ccgccagggc
     1141 gcgtcagggt gttttagcgg gtttcggggc gcagccctga accagtcacg tagcgatagc
     1201 ggagtgtata ctggcttaac tatgcagcat cagtgcggat tgtatgaaaa gtgcaccatg
     1261 accagtgtga aataccgcac agatgcgtaa ggagaaaatg cacgttccgg cgcttttccg
     1321 cttcctcgct cactgactcg ctacgctcgg tcgttcggct gcggcgagcg gtactgactc
     1381 actcaaaaac gataatacag ttatccacag aatccgggga taagaccgga aagaacatgt
     1441 gcgcaaaaag gcaaagccca acaaaaggcc acgccgatgg cgtttttcca taggctccgc
     1501 ccccctgacg agcatcacaa aaaccgacgc tcaagtcaga ggtggcgaaa cccgacagga
     1561 ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc
     1621 ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     1681 agctcacgct gttggtatct cggctcggtg taggtcgttc gctccaagct gggctgtgtg
     1741 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     1801 aacccggtaa gacacgactt agcgccactg gcagcagccg ttggtaactt ggttagcaga
     1861 gcgatgatgg cgcaaatggt gcaacagagt tcttgaagta gtggcccgac tacggctaca
     1921 ctggaaggac agtatttggt atctgcgctc tgctgaagcc agttacctcg gttaagcagt
     1981 tccccaactg acttaacctt cgatcaaacc gcctccccag gcggtttttt cgtttacagg
     2041 cagcagatta cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctactgaa
     2101 cagagatccc cgtcaattta gaagaagatg atggagccac agtccctccc tgaacatcac
     2161 gtatatagtt agcctgacat ccaacaagga ggtttatagc gaatattccc acaaaaaatc
     2221 ttttcctcat aactcgatcc ttataaaatg aaaagaatat ataacgaggt ttaatttatg
     2281 agtttaagat actatataaa aaatattttg tttggcctat actgcgcact tatatatata
     2341 taccttataa caaaaaacaa cgaagggtat tatttcctag cgtcagataa gatgctatac
     2401 gcaatagtga taagcactat tctatgccca tattcaaaat atgctattga acacatattt
     2461 tttaagttca taaagaaaga ttttttcaga aaaagaaaaa acctaaataa tgcccccgtg
     2521 gcaaaattaa acctatttat gctatacaat ctactttgtt tggtcctagc aatcccattt
     2581 ggattgctag gactgtttat atcaataaag aataattaaa tacccaacac ctcatttata
     2641 gtattaagtt tattcttatc aataaaggca catagaatgc ctgtaacaat agcaatcccc
     2701 cagataccta atgtagttcc agcaagcaca ctaaaaagta aaacaacaac ataactaact
     2761 ccagcatcta cagctttctt ctctaatgta agaaatagcg gcttccagtc acctgtatcc
     2821 ttaattttta ggatatcaga taccacatca tatccaaaag aaacatgtcc cgtaatcttc
     2881 aagtacttgg caaactgatc taaatgctta gcccagtctt catacttaac cgcctccagt
     2941 gcattgaaaa ttgcatcacg gtctgctttg ctgaatttct tatttaatac atccttgtat
     3001 ttctcaaaag cagctagagc ttcattcaca ttgctgattt tcttaccttt agatttatca
     3061 gcaagttcct gtgccatttt tgaatatttt tcaccatatt tttcagatag cgtttgataa
     3121 aagctaactg ttgcatccac agcatcctta atctgcgagt tcaggagatt agtctgtgct
     3181 gttttcaatt tatcttcagc atcatgaata cgtgaaactg ctgtacttcg cttattatta
     3241 gcctgagaaa tagcctcttg gattccattt atctcagagc taatctggtt aagacgcgtt
     3301 tctgatgctg ttacctgctt ttgtttttcc tccatctcat caccagctct cgcccgtagt
     3361 ctggtggcct caaaaaaagg acgactctga agcggatcat tcgccctagg agataaaagt
     3421 ttaacccttt catccagttc tttatattta gcagatgcct gatccaactc atttcgtttt
     3481 ccggacagcg tattcgtttc tgcatcacgg gcatgaatac tggagcttaa acgggtattg
     3541 agcgtattaa tctcttcatc cactttcgcc agctcagatt gtgcagcagc aagatttttt
     3601 tgtgccacct ccacagcccg ggcctcttca ctcaatgctg ccaggcgttt ctcttcatcc
     3661 tcagccagtt tcaattggcg ttctgtttca gcctgctcct tctctatctc tttacgtcgt
     3721 tgttctgctt cctgaaaagc cttttccgca gcttccgctt ctttacgggc tttttcttct
     3781 gcttttgcaa ggcgcaaccg ctctgcttct gcctgcatcg ctgcattatt ggcatgagcc
     3841 aggtcaataa cctccggatg agtggaatta tggcgaagcg cctcattcac aatatccttc
     3901 agatgttgag tcagcgcatc ccggtttgct tttgctttag cctgtgcttc tgcggcagct
     3961 tttgctcggg cagcctgttc tgcctgcgtt ttcttcaatt gagcagtaga ccatttagct
     4021 gtggcatgaa tggctgcaga actttcactt ttgctacctc cagttccacc accaccgcca
     4081 gagccactcc cgtctggatt accattcaaa agagtaatga ttacctgccc cttatcatca
     4141 taaggaacac catctttata gtacgctaca gctgtttcca ttataaaatc ctctttgaca
     4201 ttaaaaacaa atagttaaaa gcagtatact gtatatataa tcactggttt tatatacagt
     4261 ttaaaattac gccgctgcat tttccctgtc aaccctgtgg attttcattt ttgtgaaaac
     4321 gatcaaaaaa acagccaccc acaccacgtg ctatttccac ccgatgccac aaaaaccagc
     4381 acaaacatta ccgttctcag acctcattat gttttactga aaccatgaga tgagacacct
     4441 atgggacact gtaactttat ggcatggcac acactccggg acgcactgaa aatgactgga
     4501 agatcgcgtt cacagtttta ccgtgatatg cgctcaggtc ttgtcagtta ccgtaccagc
     4561 caggacggac gacgggagtt tgaaaccagt gaactgatcc gggcatacgg cgaattaaag
     4621 cggaatgaga caccagaaag gcacactcaa ggacactcag aaaaacctca tgatcagcag
     4681 acagaacgca ttctccggga actgaatgag ctgaaacaat gcctgacgct gatgcttgag
     4741 gataaacaag cccaggatac ggagcgccgg cgccaggaag cagaacggaa acagctacag
     4801 aatgagatag cccagctcag gcaggctctg gagcaggaaa agaaacgggg attctggtcc
     4861 aggctgttcg gtcactgaac gcgctcagaa actgatgata agataatctt cggataataa
     4921 ctcaccgaga ataaatactt taaggtaggg agacactcat gagacgtacc ggaaacaaac
     4981 tttgtcttat cgccatgata acagcaacag tagctctcac agcctgtacc ccaaagggca
     5041 gcgtggaaca acatacccgg cattacgtat atgcttctga tgacggtttt gatcccaact
     5101 tttccaccca aaaagccgac acaacacgaa tgatggtgcc tttttttcgg cagttctggg
     5161 atatgggagc taaagataaa gcgacaggaa aatcacggag tgatgtgcaa caacgcattc
     5221 aacagtttca cagccaggaa tttttaaact cactccgggg tacaactcaa tttgcgggta
     5281 ctgattaccg cagcaaagac cttaccccga aaaaatccag gctgctggct gacacgattt
     5341 ctgcggttta tctcgatggc tacgagggca gacagtaagt ggatttacca taatccctta
     5401 attgtacgca ccgccgaaac gcgttcggtg cgatcacggc agcagacagg taaaaatggc
     5461 aacaaaccac ccggaaaact gccgcgatcg cacccggtaa attttaacca catgcatacc
     5521 tatgcagcca ggtgaatcac gcaggaattg ccagtcagag accgctgaaa cggatttttt
     5581 tcatactttc ggaagcgaag aagacgggga tttgagcagg aaaacagaag ttcaggggaa
     5641 tgagcgcgat ctggcaatag aggcaaaaac acgactatga aagacacacc agaatcgcgc
     5701 ccgtatgcgt tttaacgcgt tcctgtgttt tcagcaaggt ttatgactga agcgcgttcc
     5761 cggtgccccg aaccaaccat tatcccaaaa aatgcaccgg aaacgcgctg acaacatttt
     5821 agcctgtctc tgattaccat cccagcgaag ggccatccag tgtccgttcc tgtatttcca
     5881 gctggcgctc acgctccagg gataactcat gttcgcgttc ctgtatcagc cgttcgtccc
     5941 ttatctcctg ttctcgctgt ataactggct caagcgtctg ccaggcatca attctcggcc
     6001 tgtctgcccg gtcgtagtac ggctgtaggc gttttccggt ctccagctcc atgttcggta
     6061 tgacaaaatt cagctcaagc cgtcccgtct gccaggcatc aattctcggc ctgtctgccc
     6121 ggtcgtagta cggctgtagg cgttttccgg tctccagctc catgttcgga atgacaaaat
     6181 tcagctcaag ccgtcccttg tcctggtgct ccacccacag gatgctgtac tgatttt
//
