LOCUS       NZ_CP054350             4064 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-176 plasmid pSCU-176-5, complete
            sequence.
ACCESSION   NZ_CP054350
VERSION     NZ_CP054350.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943547
            Assembly: GCF_013315675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4064)
  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  JOURNAL   Unpublished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 4064)
  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                   :: 100x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:58:56
            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)                     :: 4,962
            CDSs (total)                      :: 4,848
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 88 of 228
            Pseudo Genes (incomplete)         :: 149 of 228
            Pseudo Genes (internal stop)      :: 51 of 228
            Pseudo Genes (multiple problems)  :: 52 of 228
            Pseudo Genes (short protein)      :: 3 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054350.1.
            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..4064
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-176"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-176-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(join(3702..4064,1..1797))
                     /gene="mobQ"
                     /locus_tag="HPE52_RS24535"
                     /old_locus_tag="HPE52_24520"
     CDS             complement(join(3702..4064,1..1797))
                     /gene="mobQ"
                     /locus_tag="HPE52_RS24535"
                     /old_locus_tag="HPE52_24520"
                     /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_042042005.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRNEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRTERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREVPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            1976..2230
                     /gene="mobC"
                     /locus_tag="HPE52_RS24540"
                     /old_locus_tag="HPE52_24525"
     CDS             1976..2230
                     /gene="mobC"
                     /locus_tag="HPE52_RS24540"
                     /old_locus_tag="HPE52_24525"
                     /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_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2762..3454
                     /locus_tag="HPE52_RS24545"
                     /old_locus_tag="HPE52_24530"
     CDS             2762..3454
                     /locus_tag="HPE52_RS24545"
                     /old_locus_tag="HPE52_24530"
                     /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_044326273.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRCTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1440..1798)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          1799..1975
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2763..3454
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.821"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..1884)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.045"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atccacgccc atgaccagca aaagctgaag ctggcgggtt tcccggtcga cagaactcat
       61 taccggcatc agcgtcggtg gcagacgtcc ctgcgtaaaa tccaccttcc ttgctgccag
      121 tgatggcatg gctggctggc ggtcttctcc aagacagaaa gactccggcc atgtcttcgg
      181 ctggcggaga ttgcgggtat attgcggcca tgtctggcaa acctgcgtca gaagttgctc
      241 aaaggtcgca gaggaataaa cacgttgcag tggtggatgt tgaccgattt cgcttcggtc
      301 acagatataa ccactcctgt cacgcattaa atcaacacgc tcaaagattc tggtgcggta
      361 tttctccagc tcgttccccc agagcgtgta ttctccgttc cggttgtgaa gcagaaggta
      421 acaggtcatt tccccgttac caggcatggg ggcctcgcca taccccgtaa cgactgcgct
      481 cagtacccct gaatccataa cggcattgtc atttttcctg agctgttccg ctcgtcgctc
      541 cgtgcgacta cgttctgtat cctcctgctc cttccggcgc aattcctctt cacgtttaag
      601 caactggact ctgagagctg caaggccgga tgccccccac tgctgccact gtttttcaaa
      661 tgccgtctga ctcgcgggaa tgtcctgttt ctccaccttc cggtaatgct gtcgcaattt
      721 ttccatttgc tggctcagcg actgaatttt tccctgttcg ttacggtatt ccggtgccgc
      781 ccattgcatc aggggaatac gggaaaaacc ggacgaaaac ggtgatgatt ttttcaggct
      841 ggcagcatgg ctcatcgctt cctttcgttc ggtgttcagc tcttcccagc gtctgcgcgt
      901 cgcctgcata tctgccatca tcgacatggc attactggtg agtttccatg ccgcattact
      961 gtccttcggc aacgcttcga tgatgtcacg tagtgtgtac gaagttgcgt tgtcaggaag
     1021 cacgatattc agaaggtcag ccacacggcg ggcaggctct gtcagcccgc tgttcctgag
     1081 ttcagtgcgg gaaatctgta tttccaggtt aagcctgtta atcagacgat tctgttcgcc
     1141 gcgttctgtt tcgataccgc gtgtttccat cgcacaggca gactttccga ggtgaatacc
     1201 aggcgttttc tcaagcccct gtcgctcgta tgaacgatgg tctatctctt cctgataacc
     1261 ggcgttcgcc agtgctctgt ttgcatggtc agcccatgat gcacgccacg tctcggcatg
     1321 tgtccggtcg ttccagtccc tgacctttcc gccgaaccca gcaggtccga cagccctcgt
     1381 ggtcagcatg atgtgcgcat ggggatttgt tttatccatg tgatggaacg ccacatcagc
     1441 aatcatgccc tgactgacaa agttttctct gacaaaggcg agaacggttt cccgtgcggc
     1501 atcctgcggc agttcacggg ggatagcgag ttcaatttcc cgcgcaagtt gtgagttctt
     1561 ccggcgttcg gccttctcaa cggcattcca gagttcggca cggttcgtac accaggcagg
     1621 ggctgtcgcg ggggtcagaa tcacagcttc agccacaccg cttttgcggg tgtagtcgtg
     1681 agtcagtccg gtacgctcat caagcatcag tgaaccggaa cgataggcag cggaagctac
     1741 ggcgctgtag ccgctgcttc tggagataat tttcatgctg agatgataaa tcgccatttc
     1801 tgccgtaatg cctttttgta gttttctttc agccccgcag ggcgcacaca atcgaaacgg
     1861 agtggagatt gtataagtgc gcacttcgtg atttgccgtg cattatgcca gctcagtttt
     1921 taaactacca gtgacgcgct aaaatgcgat ttttcatcgc gcacggagtt acatcatgag
     1981 cagaacgctc gaacagaaga ttgctgatgc tgaggcgaga ttacagcgcc tgaaggcgaa
     2041 gagccggagc ttggacacag cgcagaaggt tgttgtgggt gcagcattgc tggcaaaggt
     2101 cagaaagccg gaggaggtgc agttgcgtgc ctggttactc cagttcctga aggcagaggt
     2161 gacacgacag gctgatgtga cgcgcatact gccgctgatt aacgagctgg aggcgctgcc
     2221 aggacagtga ttgtatcgtc cgctcgccgc agccccagcg accgagcgtt agcgagcgag
     2281 tgggcgagga agcggaagtg aatccgtcgc caggttgagc acatacgcac ggtttttcgg
     2341 caggtgatat gcgctgaacc cgcatgaata ctggatttcc acagggttgg aaggggagta
     2401 ttcggaactt gcaattctac tttcttgcaa cacattgttt ttatttgttt tttgttttca
     2461 gcaccccaag ttatccacag gctcgccgtt aagtttttag atcttgtttt taagatcttg
     2521 tttttaatac ttgttttagg ggcgaaattc attaataaaa tcaatatgtt gcagtggtat
     2581 atgtggagga atttaaggta tatgtggagg aatttaaggt gtttaggtgg aggaatttaa
     2641 ggtaaaggtg gaggaattta aggtgttatt cacagaaatg tgaggatata aaaaaaaata
     2701 ttccacattt cttatttgtg gggcacatta aagcatcacc acatttgaac gggatctttg
     2761 tatgtcggac ttgattgcct acaagtcgaa tgctttggtt gaggccagct acaagttgac
     2821 cctacaggaa caacgttttc tgttgctgtg tatcagtcga ttgaaatctg gtgctgatgc
     2881 tgaattgcaa aagacaatga ccattaccgc tgcggaatat tttgattcat tccctgacat
     2941 ggggcggaaa aatgccgagg ttcagttaca ggaagcgatc gatcgtttat gggacaggtc
     3001 gatcattctc aagaatgacg agaagcgtga ggagttccgc tggatccagt atcgggcaca
     3061 gtacgctaaa ggtgaggcca aggctcgaat aaccttttct gacgcggtaa tgccttatct
     3121 gacgcaactg aaggggcaat tcacgcgcgt tgttataaaa aacatatcag gtttatcaag
     3181 tagttacagt ataagaatat acgagttcct ccagcaattc cgctgtacgg gagagagaat
     3241 tattgctctt aatgactttc gttcaatgtt agggattgaa aataaataca aacaattcag
     3301 agacttaaat aaaatactaa taaaaccctg tgttgacgaa ctgaacaaaa aaagcgacct
     3361 ggctgtaacg gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt
     3421 caaggaagac aaacagatca agatgacgat ctaaaatcga ttttaatgca cctaaaacgc
     3481 tccctgctgc gttttttttg tgttagtagt gcgaaggtac tattgaagtg aaaaattgcg
     3541 ccaaaaacgc tctgatgcag cgaaaaaaga acccccaatt tttgggggcg gaaaaacaaa
     3601 actatgcttg cgttatgtga gtgtgcttct tgcattcatc cctgtcgatg aacatcgacg
     3661 aacataacac gatgttaaac aaaacaaaat attgttcaca ttcactgtga ccaaccgcga
     3721 tcatgtctcc tctcggtggt gtgtgttctt gcatcttcct cgcgccgcca ttcgtcccag
     3781 gtacgattga aacccagcga gcggaacaga tgatccggct gtttttctgg tgtgttgacg
     3841 gcagcaaaaa gcggtacctc acgggttttc agatgaaact ccataagttc cggcgcaggt
     3901 gatatgtggc tgtctgcatc gtgatttacg gcaacaccat accctgcata ccgtaacccc
     3961 ttatcggtca gtgcactgat gaccagctgg ctgttatcgg ctgagggaac ggcaaacgcg
     4021 ggatacagcg taccattaag ccggacaaca ccgcccagag agtc
//
