LOCUS       NZ_CP053242             4067 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-106 plasmid pSCU-106-8, complete
            sequence.
ACCESSION   NZ_CP053242
VERSION     NZ_CP053242.1
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 4067)
  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  JOURNAL   Unpublished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 4067)
  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
            CP053242.1.
            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..4067
                     /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-106-8"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            <1..217
                     /locus_tag="HHJ24_RS26915"
                     /old_locus_tag="HHJ24_26910"
                     /pseudo=""
     CDS             <1..217
                     /locus_tag="HHJ24_RS26915"
                     /old_locus_tag="HHJ24_26910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011264043.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=2
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(460..1167)
                     /locus_tag="HHJ24_RS26920"
                     /old_locus_tag="HHJ24_26915"
     CDS             complement(460..1167)
                     /locus_tag="HHJ24_RS26920"
                     /old_locus_tag="HHJ24_26915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1698..1952)
                     /gene="mobC"
                     /locus_tag="HHJ24_RS26925"
                     /old_locus_tag="HHJ24_26920"
     CDS             complement(1698..1952)
                     /gene="mobC"
                     /locus_tag="HHJ24_RS26925"
                     /old_locus_tag="HHJ24_26920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091749.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            2131..>4067
                     /gene="mobQ"
                     /locus_tag="HHJ24_RS26930"
                     /old_locus_tag="HHJ24_26925"
     CDS             2131..>4067
                     /gene="mobQ"
                     /locus_tag="HHJ24_RS26930"
                     /old_locus_tag="HHJ24_26925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_170969621.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPEDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCLTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDA"
                     /name="mobQ"
     Typing          complement(1957..2130)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="98.0"
                     /evalue="2.6299999999999998e-81"
     Typing          2131..2489
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          complement(461..1167)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2045..4065
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.345"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cagccacata tcacctgcgc cggaacttat ggagtttcat ctgaaaaccc gtgaggcacc
       61 gctttttgct gtcgtcaaca caccagaaaa acagccggat catctgttcc gctcgctggg
      121 tttcaatcgt acctgggacg aatggcggcg cgaggaagat gcacgaacac acgccaccga
      181 gaggagacct gatcgcggtt ggtcacaggg aatgtgaaca atattttgtt ttgtttaaca
      241 tcgtgttatg ttcgtcgatg ttcatcgaca gggatgaatg caagaagcac actcacatag
      301 cgcaaacata gttttgtttt tccgccccca aaaattgggg gttctttttt ttgctgcatc
      361 agagcgtttt tgacgcaact tttcacttca atagtacctt cgcattcctg acacaagaaa
      421 aacgcgacag tgagcgtttt aggtgcctta aaatcgattc tagatcgtca tcttgatctg
      481 tttgtcttcc ttgaagcgaa aatgcagggc tacaaccgtg cgcccctttt tgatcgtctc
      541 aaccgttaca gccaggtcgc tttttttgtt cagttcgtca acacagggtt ttattagatc
      601 cctgtttaac gttttgaaat ctttatattt accatcaagc atcagtgatg atttaaaatc
      661 atcgagggcg ataatacgtt ccccagtact gcggaattgc tggagaattt cgtatattct
      721 tatgctgtaa cttcttgata aattagaaat atttttaatg acgactctgg tgaattgccc
      781 cttcaactgt gtcagataag gcattaccgc gtcagaaaaa gtgatttgtg ctttcccctc
      841 tcccctcgcg tactgtgccc gatactgaat ccagcggaac tcctcgcgct tctcgtcgtc
      901 cttgagaatg atcgacctgt cccacaaacg atcgatcgct tcctgtagct gaacctcggc
      961 atttttccgc cccatatcag ggaatgaatc aaaatattcc gcagctgtaa tggtcattgt
     1021 cttttgcaat tcaggtgaag ctacgtcagt accggagtta agtcggctta tgcagagcaa
     1081 taagaaacgc tgttcttgta aagttagctt gtaactggcc tcaaccagcg cattggactt
     1141 ataggctatc agagggtttg atgtcatttt aaccaccagg ccaaaaatga ggtgaaataa
     1201 aaacctatca cctttagcat tggtgagcaa ttatattttc accccccatt ttcctgtgaa
     1261 tattacctta aatctcctca cctttacctt aaattacctc acccaagcac cttaaattat
     1321 atcaccttta ccttaaattc ccccacctat gcacgtgtaa cgcattgttt ttaatcagga
     1381 atttcgaccc taaaacaagt attaaaaaca agatcttaaa aacaagatct aaaaacttaa
     1441 cggcgagcct gtggataact tggggtgctg aaaataaaaa tcaaataaaa acaatgtatt
     1501 gcaaaaaatc aggattgaaa attccgaata caccccctcc aaccctgtgg aaatccagta
     1561 ttcatgcggg ttcagcgcat atcacctgtc gaaaaaccgt gcgtatgtgc tcaacctggc
     1621 gactgattca cttccgcttc ctcgcccact cgctcgctaa cgttcggtcg ctgggctgcg
     1681 gcgagcggac gatacaatca ctgctctggc agcgcctcca gctcgttaat cagcggcagt
     1741 attcgcgtca catcagcctg ccgtgtcacc tctgccttca ggaactggag taaccaagct
     1801 cgcaactgca cttcctccgg ctttctgacc tttgccagca atgctgcacc cacaatgacc
     1861 ttctgcgctg tgtccaggct ccggctcttc gccttcaggc gctgtaatct ggcctcagct
     1921 tcggcaatct tctgttcgag tgttctgctc atttcgtgac tccgtgcgcg gtgaaaaatc
     1981 gcattttagc gcgtcactgg tagtttaaaa actgagctgg cataatgcac ggcaaatcac
     2041 gaagtgcgca cttatacaat ctccactccg tttcgattgt gtgcgccctg cggggctgaa
     2101 agaaaactgc aaaaaggcat tacggcagaa atggcgattt atcatctcag tatgaaaatc
     2161 atctccagaa gcaacggcta cagcgccgtt gcttctgctg cctatcgttc tggttcacta
     2221 atgcttgatg agcgtaccgg actgactcac gactacaccc gcaaaagcgg tgtggctgag
     2281 gctgtgattc tgacccccgc gacagcccct gcctggtgta cgaaccgtgc cgaactctgg
     2341 aatgccgttg agaaggccga acgccggaag aactcacaac ttgcgcggga aattgaactc
     2401 gctatccccc gtgaactgcc gcaggatgcc gcacgggaaa ccgttctcgc ctttgtcaga
     2461 gaaaactttg tcagtcaggg catgattgct gatgtggcgt tccatcacat ggataaaaca
     2521 aatccccatg cgcacatcat gctgaccacg agggctgtcg gacctgctgg gttcggcgga
     2581 aaggtcaggg actggaacga ccggacacat gccgagacgt ggcgtgcatc atgggctgac
     2641 catgcaaaca gggcactggc gaacgccggt tatcaggaag agatagacca tcgttcatac
     2701 gagcgacagg ggcttgagaa aacgcctggt attcacctcg gaaagtctgc ctgtgcgatg
     2761 gaaacacgcg gtatcgaaac agaacgcggc gaacagaatc gtctgattaa caggcttaac
     2821 ctggaaatac agatttcccg caccgaactc aggaacagcg ggctgacaga gcctgcccgc
     2881 cgtgtggctg accttctgaa tatcgggctt cctgacaacg caacttcgta cacactacgt
     2941 gacatcatcg aagcgttgcc ggaggacagt aacgcggcat ggaaactcac cagtaacgcc
     3001 atgtcgatga tggcagatat gcaggcgacg cgcagacgct gggaagagct gaacaccgaa
     3061 cgaaaggaag cgatgagcca tgctgccagc ctgaaaaaat catcgccgtt ttcgtccggt
     3121 ttttcccgta ttcccctgat gcaatgggct gcaccggaat accgtagtga gcagggaaaa
     3181 atccagtctc tgagccagca aatggaaaaa ttgcgacagc attaccggaa ggtggagaaa
     3241 caggacattc ccgcgagtca gacggcattt gaaaaacagt ggcagcagtg gggggaatcc
     3301 ggccttgcag ctctcagatc ccagttgctt aaacgtgaag aggaattgcg ccggaaggag
     3361 ctggaggata cagaacgtag tcgcgcggag cagctcagaa aaaatgacaa tgccgttatg
     3421 gattcagggg tgctgagagc agtcgttacg gggtatggcg aggctcccat gcctggtaac
     3481 ggggaaatga cctgttacct tctgcttcac aaccggaacg gagaatatac gctctggggg
     3541 aacgagctgg agaaataccg caccaggatc tttgagagtg ttgatttaat gcgtgacagg
     3601 agtggttata tctgtgaccg aagcgaaatc ggtcaacatc caccactgca acgtgtttat
     3661 tcctctgcga cctttgagca acttctgacg caggtttgcc tgacatggcc gcaacatacc
     3721 cgcaatctcc gccaaccgaa gacatggccg gagtctttct gtcttggaga agaccgccag
     3781 ccagccatgc catcactggc agcaaggaag gtggatttta cgcagggacg tctgccaccg
     3841 acgctgatgc cggtcatgag ttctgtcgac cgggaaaccc gccagcttca gcttttgctg
     3901 gtcatgggcg tggatgactc tctgggcggt gttgtccggc ttaatggtac gctgtatccc
     3961 gcgtttgccg ttccctcagc cgataacagc cagctggtca tcagtgcact gaccgataag
     4021 gggttacggt atgcagggta tggtgttgcc gtaaatcacg atgcaga
//
