LOCUS       NZ_CP051748             4082 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-484 plasmid pSCU-484-4, complete
            sequence.
ACCESSION   NZ_CP051748
VERSION     NZ_CP051748.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609800
            Assembly: GCF_012934785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4082)
  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  JOURNAL   Unpublished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 4082)
  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                   :: 38x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 02:28:45
            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)                     :: 5,085
            CDSs (total)                      :: 4,969
            Genes (coding)                    :: 4,723
            CDSs (with protein)               :: 4,723
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 246
            CDSs (without protein)            :: 246
            Pseudo Genes (ambiguous residues) :: 0 of 246
            Pseudo Genes (frameshifted)       :: 148 of 246
            Pseudo Genes (incomplete)         :: 121 of 246
            Pseudo Genes (internal stop)      :: 52 of 246
            Pseudo Genes (multiple problems)  :: 61 of 246
            Pseudo Genes (short protein)      :: 3 of 246
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051748.1.
            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..4082
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-484"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-484-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            complement(join(4065..4082,1..684))
                     /locus_tag="HHJ53_RS25125"
                     /old_locus_tag="HHJ53_25135"
     CDS             complement(join(4065..4082,1..684))
                     /locus_tag="HHJ53_RS25125"
                     /old_locus_tag="HHJ53_25135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1217..1471)
                     /gene="mobC"
                     /locus_tag="HHJ53_RS25130"
                     /old_locus_tag="HHJ53_25140"
     CDS             complement(1217..1471)
                     /gene="mobC"
                     /locus_tag="HHJ53_RS25130"
                     /old_locus_tag="HHJ53_25140"
                     /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_052992135.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVMRILPLINELEALPGQ"
                     /name="mobC"
     gene            1650..3809
                     /gene="mobQ"
                     /locus_tag="HHJ53_RS25135"
                     /old_locus_tag="HHJ53_25145"
     CDS             1650..3809
                     /gene="mobQ"
                     /locus_tag="HHJ53_RS25135"
                     /old_locus_tag="HHJ53_25145"
                     /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_001029343.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(1473..1649)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1650..2008
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..684)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          1564..3806
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.866"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtttgtct tccttgaagc gaaaatgcag ggctacaacc gtgcgcccct ttttgatcgt
       61 ctcaaccgtt acagccaggt cgcttttttt gttcagttcg tcaatgcagg gtcttaataa
      121 ttgctggtta agtgatttat atgtttgata tttatgctct atatcaagca ttgagcgaaa
      181 atcatcgaga gcgataatac gttcgccagt actgcggaac tgctggagga gttcgtatat
      241 ccttatactg taacttcttg ataatctaga tatattcttg attacaactc tagtaaattg
      301 cccttgtagt tgtgtcaaat aaggcattac tgcgtcagaa aatgttattt gtgctctggc
      361 ctcgccttta gcgtactgtg cccgatactg gatccagcgg aactcctcac gtttctcgtc
      421 atccttgaga atgattgacc tgtcccacaa acgatcaatt gcttcctgta actgaacctc
      481 ggcatttttc cgccccatgt cagggaatga atcgaaatat tccgcagctg taatggtcat
      541 tgtcttttgc aattttggag attctgcatc agccccagac ttcaatcgac cgatgcaaag
      601 taacaaaaat cgctgttcct gtagggtcaa tttataactg gcttcaacca gcgcattgga
      661 tttataggca attagatccg acatagagca tccctcccca aaaggtaatg aataaaagat
      721 aaacataccc tcaacgaaag gcaatgcctt tttattttaa tatccctttt tctgtgaata
      781 ttaccttaaa tcatattgcc tttaccttaa attcccccac ctaaacacct taaatcatat
      841 tacctttacc ttaaatcaca ttacctatag cattgtaaca ttttgttttc tataaggaat
      901 tttggcgcta aaacaagtat taaaaacaag atcttaaaaa caagatctaa aaacttaacg
      961 acgagcctgt ggataacttg gagtgctgaa aacaaaaaac caataaaaac aatgcgttgc
     1021 aaaaaagcag aattgcaagt tccgaataca ccccctccaa ccctgtggaa atccagtatt
     1081 catgcgggtt cagcgcatat cacctcccga aaaaccgtgc gtatgtgctc aatcaggcga
     1141 cggattcact tccgcttcct cgcccactcg ctcgctaacg ctcggtcgct gggactgcgg
     1201 cgagcggacg atacaatcac tgtcctggca gcgcttccag ctcgttaatc agcggcagta
     1261 tgcgcatcac atcagcctgt cgtgtcacct ctgccttcag gaactggagt aaccaggcac
     1321 gcaactgcac ctcctccggc tttctgacct ttgccagcaa tgctgcaccc acaatgacct
     1381 tctgcgctgt gtccagactc ctgctcttcg ccttcaggcg ctgtaatctg gcctcagcat
     1441 cagcaatctt ctgttcgagt gttctgctca tgatgtaact ccgtgcgcga tgaaaaatcg
     1501 cattttagcg cgtcactggt agtttaaaaa ctgagctggc ataatgcacg gaaaatcacg
     1561 aagtgcgcac ttatacaatc tccactccgt ttcgattgtg tgcgccctgc ggggctgaaa
     1621 gaaaaccaca aaaaggcatt acggcagaaa tggcgattta tcatctcagc atgaaaatca
     1681 tctccagaaa cagcggctac agcgccgttg cttctgctgc ctatcgttcc ggttcactga
     1741 tgcttgatga gcgtaccgga ctgactcacg actacacccg caaaagcggt gtggctgaag
     1801 ctgtgattct gactcccgcg acagcccctg cctggtgtac gaaccgtgcc gaactctgga
     1861 atgccgttga gaaggccgaa cgccggaaga actcacaact tgcgcgggaa attgaactcg
     1921 ccatcccccg cgaactaccg caggatgccg cacgggaaac cgttctcgcc tttgtcagag
     1981 aaaactttgt cagtcagggc atgattgctg atgtggcgtt ccatcacatg gataaaacaa
     2041 atccccatgc gcacatcatg ctgaccacga gagctgtcgg acctgctgga ttcggtggaa
     2101 aggtcaggga ctggaacgac cggacacatg ccgagacgtg gcgtgcatca tgggctgacc
     2161 atgcgaacag ggcactggcg aacgccggtt atcaggaaga gatagaccat cgttcatacg
     2221 agcgacaggg gcttgagaaa acgcctggta ttcacctcgg aaagtctgcc tgtgcgatgg
     2281 aaacacgcgg tatcgaaaca gaacgcggcg aacagaatcg tctgattaac agacttaacc
     2341 tggaaataca gatttcccgt accgaactca gaaacagcgg gctgacagag cctgcccgcc
     2401 gtgtggctga ccttctgaat atcgtgcttc ctgacaacgc aacttcgtac acactacgtg
     2461 acatcatcga agcgttgccg aaggacagta atgcggcatg gaaactcacc agtaatgcca
     2521 tgtcgatgat ggcagatatg caggcgacgc gcagacgctg ggaagagctg aacaccgaac
     2581 gaaaggaagc gatgagccat gctgccagcc tgaaaaaatc atcgccgttt tcgtccggtt
     2641 tttcccgtat tcccctgatg caatgggcgg caccggaata ccgtagcgaa cagggaaaaa
     2701 tccagtcgct gagccagcaa atggaaaaat tgcgacagca ttaccggaag gtggagaaac
     2761 aggacattcc cgcgagtcag acggcatttg aaaaacagtg gcagcagtgg ggggcatccg
     2821 gccttgcagc tctcagagtc cagttgctta aacgtgaaga ggaattgcgc cggaaggagc
     2881 aggaggatac agaacgtagt cgcgcggagc gacgagcgga acagctcagg aaaaatgaca
     2941 atgccgttat ggattcaggg gtactgagcg cagtcgttac ggggtatggc gaggccccca
     3001 tgcctggtaa cggggaaatg acctgttacc ttctgcttca caaccggaac ggagaataca
     3061 cgctctgggg gaacgagctg gagaaatacc gcaccagaat ctttgagcgt gttgatttaa
     3121 tgcgtgacag gagtggttat atctgtgacc gaagcgaaat cggtcaacat ccaccactgc
     3181 aacgtgttta ttcctctgcg acctttgagc aacttctgac gcaggtttgc cagacatggc
     3241 cgcaatatac ccgcaatctc cgccagccga agacatggcc ggagtctttc tgtcttggag
     3301 aagaccgcca gccagccatg ccatcactgg cagcaaggaa ggtggatttt acgcagggac
     3361 gtctgctacc gacgctgatg ccggtaatga gttctgtcga ccgggaaacc cgccagcttc
     3421 agcttttgct ggtcatgggc gtggatgact ctctgggcgg tgttgtccgg cttaatggta
     3481 cgctgtatcc cgcgtttgcc gttccctcag ccgataacag ccagctggtc atcagtgcac
     3541 tgaccgataa ggggttacgg tatgcagggt atggtgttgc cgtaaatcac gatgcagaca
     3601 gccacatatc acctgcgccg gaacttatgg agtttcatct gaaaacccgt gaggcaccgc
     3661 tttttgctgc cgtcaacaca ccagaaaaac agccggatca tctgttccgc tcgctgggtt
     3721 ttaatcgtac ctgggacgaa tggcggcgcg aggaagatgc acgaacacac gccaccgaga
     3781 ggagacatga tcgcggttgg tcacagtgaa tgtgaacaat attttgtttt gtttaacatc
     3841 gtgttatgtt cgtcgatgtt cttcgatgtt catcgacagg gatgaatgca agaagcacac
     3901 acataatgca agcatagttt tgtttttccg cccccaaaaa atgggggttc ttttttcgct
     3961 gcattagagc gcttttgacg caatttttca cttcaatagt accttcgcac tactaacaca
     4021 aaaaaaacgc agcagggagc gttttaggtg ccttaaaatc gattttagat cgtcatcttg
     4081 at
//
