LOCUS       NZ_CP053254             4074 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain SCU-204 plasmid pSCU-204-3, complete
            sequence.
ACCESSION   NZ_CP053254
VERSION     NZ_CP053254.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609789
            Assembly: GCF_013085905.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  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  JOURNAL   Unpublished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 4074)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Hess,D. and Pandori,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
  REMARK    Nucleotide sequence updated by submitter
REFERENCE   3  (bases 1 to 4074)
  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                   :: 155.0x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 04:36:16
            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)                     :: 5,285
            CDSs (total)                      :: 5,165
            Genes (coding)                    :: 4,920
            CDSs (with protein)               :: 4,920
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 245
            CDSs (without protein)            :: 245
            Pseudo Genes (ambiguous residues) :: 0 of 245
            Pseudo Genes (frameshifted)       :: 97 of 245
            Pseudo Genes (incomplete)         :: 157 of 245
            Pseudo Genes (internal stop)      :: 46 of 245
            Pseudo Genes (multiple problems)  :: 51 of 245
            Pseudo Genes (short protein)      :: 4 of 245
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053254.2.
            On Apr 28, 2021 this sequence version replaced NZ_CP053254.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-204"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-204-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2013"
     gene            join(2012..4074,1..97)
                     /gene="mobQ"
                     /locus_tag="HHJ42_RS25110"
                     /old_locus_tag="HHJ42_26125"
     CDS             join(2012..4074,1..97)
                     /gene="mobQ"
                     /locus_tag="HHJ42_RS25110"
                     /old_locus_tag="HHJ42_26125"
                     /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_211145637.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NHLINRLNLEIQISHTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(345..1046)
                     /locus_tag="HHJ42_RS25115"
                     /old_locus_tag="HHJ42_26120"
     CDS             complement(345..1046)
                     /locus_tag="HHJ42_RS25115"
                     /old_locus_tag="HHJ42_26120"
                     /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_001281396.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1579..1833)
                     /gene="mobC"
                     /locus_tag="HHJ42_RS25120"
                     /old_locus_tag="HHJ42_26130"
     CDS             complement(1579..1833)
                     /gene="mobC"
                     /locus_tag="HHJ42_RS25120"
                     /old_locus_tag="HHJ42_26130"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(1835..2011)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2012..2370
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          complement(347..1046)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1926..4072
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.743"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gctgggtttc aatcgtacct gggacgaatg gcggcgcgag gaagatgcac gaacacacgc
       61 caccgagagg agacatgatc gcggttggtc acagtgaatg tgaacaatat tttgttttgt
      121 ttaacatcgt gttatgttcg tcgatgttca tcgacaggga tgaatgcaag aagcacactc
      181 acataacgca agcatagttt tgtttttccg cccccaaaaa ttgggggttc ttttttcgct
      241 gcatcagagc gtttttgacg caatttttca cttcaatagt accttcgcac tactaacaca
      301 aaaaaaacgc aacagggagt gttttaggtg ccttaaaatc gattctagat cgtcatcttg
      361 atctgtttgt cttccttgaa gcgaaaatgc agggctacaa ccgtgcgccc ctttttgatc
      421 gtctcaaccg ttacaaccag atcgcttttt tcgttcagtt cggcgatggc tggcttgatt
      481 atcatcttat tcaagtcttt gaattgttga tatttatctt caacggcaag catggttcgg
      541 aaatcatcga tagctatcgt tctgtcaccg gtgctgcgga actgctggag cagctcgtaa
      601 atgcggatgc tgtaggtgct ggagaggctg gagacgttct tcacgactac ccgcgtaaac
      661 tgccccttga gctgtgtcag atacggcatg atggcatcgg agaaggtgat ctctactttc
      721 gcctcacctt tgaaatactg cgcccggtac tgcacccagc ggaactcttc tcgtttttcc
      781 tcgttcttga tgattactga cctgtcccag aggcgatcta tcgcttcctt gagcctagct
      841 tcagcgtgct gccgtcccat gtcaggaaag gcatcatgaa actctgcagc cgtgatggtc
      901 atggtttttt gttcatccgg cgaaggggaa tcttctccgg atttcaggcg gctgatacag
      961 accagcagga agcgctgttc ctgcaaagtg agcttgtagc ttgcctcgat aagggcgttt
     1021 gatttgtaag ctatcagatc tgacatttcg cttgctcgtt gctattggtg gcgttttttt
     1081 actgtacgcc acccatcata ttggtggaag tttttttttt gcaacccctt ttttctgtgg
     1141 attacacccc caaaagctcc acctatcacc cccaaaagct ccacctatca cccccaaaag
     1201 ctccacctat cacccccaaa agctccacct atctcgccag aacaccttta aaatcatgtg
     1261 gttacaagac ctaaaaaggt tttaaaaaaa aagatctaaa aataagatct taaaaactta
     1321 acggcgagcc tgtggataac ttggggtgct gaaaataaaa atccaataaa aacaatgtgt
     1381 tgaaaaaaat caggattgaa gattccgaat acaccccctc caaccctgtg gaaatccagt
     1441 attcatgcgg gttcagcgca tatcacctgt cgaaaaaccg tgcgtatgtg ctcaacatgg
     1501 cgactgattc acttccgctt cctcgcccac tcgctcgcta acgctcggtc gctgggctgc
     1561 ggcgagcgga cgatacaatc actgctctgg cagcgcctcc agctcgttaa tcagcggcag
     1621 tattcgcgtc acatcagcct gccgtgtcac ctctgccttc aggaactgga gtaaccaagc
     1681 tcgcaactgc acttcctccg gctttctgac ttttgccagc aatgctgcac ccacaatgac
     1741 cttctgcgct gtgtccaggc tccggctctt cgccttcagg cgctgtaatc tcgcctcagc
     1801 atcagcaatc ttctgttcga gcgttctgct catgatgtaa ctccatgcgc gatgaaaaat
     1861 cgcattttag cgcgtcactg gtagtttaaa aactgagctg gcataatgca cggcaaatca
     1921 cgaagtgcgc acttatacaa tctccactcc gtttcgattg tgtgcgccct gcggggctga
     1981 aagaaaactg caaaaaggca ttacggcaga aatggcgatt tatcatctca gtatgaaaat
     2041 catctccaga agcaacggct acagcgccgt tgcttctgct gcctatcgtt ctggttcact
     2101 aatgcttgat gagcgtaccg gactgactca cgactacacc cgcaaaagcg gtgtggctga
     2161 ggctgtgatt ctgacccccg cgacagcccc tgcctggtgt acgaaccgtg ccgaactctg
     2221 gaatgccgtt gagaaggccg aacgccggaa gaactcacaa cttgcgcggg aaattgaact
     2281 cgccatcccc cacgaactgc cgcaggatgc cgcacgggaa accgttctcg cctttgtcag
     2341 agaaaacttt gtcagtcagg gcatgattgc tgatgtggcg ttccatcaca tggataaaac
     2401 aaatccccat gcgcacatca tgctgaccac gagggctgtc gggcctgctg ggttcggcgg
     2461 aaaggtcagg gactggaacg accggacaca tgccgagacg tggcgtgcat catgggctga
     2521 ccatgcaaac agggcactgg cgaacgccgg ttatcaggaa gagatagacc atcgttcata
     2581 cgagcgacag gggcttgaga aaacgccggg tattcacctc ggaaagtctg cctgtgcgat
     2641 ggaaacacgc ggtatcgaaa cagaacgcgg cgaacagaat catctgatta acaggcttaa
     2701 cctggaaata cagatttccc acaccgaact caggaacagc gggctgacag agcctgcccg
     2761 ccgtgtggct gaccttctga atatcgggct tcctgacaac gcaacttcgt acacactacg
     2821 tgacatcatc gaagcgttgc cgaaggacag taacgcggca tggaaactca ccagtaacgc
     2881 catgtcgatg atggcagata tgcaggcgac gcgcagacgc tgggaagagc tgaacaccga
     2941 acgaaaggaa gcgatgagcc atgctgccag cctgaaaaaa tcatcgccgt tttcgtccgg
     3001 tttttcccgt attcccctga tgcaatgggc ggcaccggaa taccgtagcg aacagggaaa
     3061 aatccagtcg ctgagccagc aaatggaaaa attgcgacag cattaccgga aggtggagaa
     3121 acaggacatt cccgcgagtc agacggcatt tgaaaaacag tggcagcagt ggggggcatc
     3181 cggccttgca gctctcagag tccagttgct taaacgtgaa gaggaattgc gccggaagga
     3241 gcaggaggat acagaacgta gtcgcgcgga gcgacgagcg gaacagctca ggaaaaatga
     3301 caatgccgtt atggattcag gggtactgag cgcagtcgtt acggggtatg gcgaggcccc
     3361 catgcctggt aacggggaaa tgacctgtta ccttctgctt cacaaccgga acggagaata
     3421 cacgctctgg gggaacgagc tggagaaata ccgcaccaga atctttgagc gtgttgattt
     3481 aatgcgtgac aggagtggtt atatctgtga ccgaagcgaa atcggtcaac atccaccact
     3541 gcaacgtgtt tattcctctg cgacctttga gcaacttctg acgcaggttt gccagacatg
     3601 gccgcaatat acccgcaatc tccgccagcc gaagacatgg ccggagtctt tctgtcttgg
     3661 agaagaccgc cagccagcca tgccatcact ggcagcaagg aaggtggatt ttacgcaggg
     3721 acgtctgcca ccgacgctga tgccggtcat gagttctgtc gaccgggaaa cccgccagct
     3781 tcagcttttg ctggtcatgg gcgtggatga ctctctgggc ggtgttgtcc ggcttaatgg
     3841 tacgctgtat cccgcgtttg ccgttccctc agccgataac agccagctgg tcatcagtgc
     3901 actgaccgat aaggggttac ggtatgcagg gtatggtgtt gccgtaaatc atgatgcaga
     3961 cagccacata tcacctgcgc cggaacttat ggagtttcat ctgaaaaccc gtgaggcacc
     4021 gctttttgct gccgtcaaca caccagaaaa acagccggat catctgttcc gctc
//
