LOCUS       NZ_CP054349             5167 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-176 plasmid pSCU-176-4, complete
            sequence.
ACCESSION   NZ_CP054349
VERSION     NZ_CP054349.1
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 5167)
  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  JOURNAL   Unpublished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 5167)
  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
            CP054349.1.
            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..5167
                     /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-176-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            join(4317..5167,1..76)
                     /locus_tag="HPE52_RS24510"
                     /old_locus_tag="HPE52_24495"
     CDS             join(4317..5167,1..76)
                     /locus_tag="HPE52_RS24510"
                     /old_locus_tag="HPE52_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_174165910.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPDRGGAKKDSGNLT
                     PTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQERTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            79..612
                     /locus_tag="HPE52_RS24515"
                     /old_locus_tag="HPE52_24500"
     CDS             79..612
                     /locus_tag="HPE52_RS24515"
                     /old_locus_tag="HPE52_24500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(678..887)
                     /locus_tag="HPE52_RS24520"
                     /old_locus_tag="HPE52_24505"
     CDS             complement(678..887)
                     /locus_tag="HPE52_RS24520"
                     /old_locus_tag="HPE52_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            2624..3538
                     /locus_tag="HPE52_RS24525"
                     /old_locus_tag="HPE52_24510"
     CDS             2624..3538
                     /locus_tag="HPE52_RS24525"
                     /old_locus_tag="HPE52_24510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(3742..4140)
                     /locus_tag="HPE52_RS24530"
                     /old_locus_tag="HPE52_24515"
     CDS             complement(3742..4140)
                     /locus_tag="HPE52_RS24530"
                     /old_locus_tag="HPE52_24515"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_122398753.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLLDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     Typing          2625..3399
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          4318..5165
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.647"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 cagagtgagc agacaggagc gaactgaacc tgaacgggtt aaatcaccgt cacgtggatt
       61 ttctatggga ttctgaacat ggccagcaca gaagaaaaat tactcacgct cctgttatcg
      121 gtggagcatc tgcaacatac cgcaatggag caacagaaag ctgttgctga ttctctggct
      181 gtggcaaggg aaacacttcg cggatatcgg gatatttctg acggcgtggc aaaacaggtc
      241 agggatgaag tccgaaatga ggtgcagaag ctggatgtgg cagggctgat aggtgagcgc
      301 atcagccagg attttcagcg gctggaagag tcagtcgcaa acatgaaggc aaacgcggat
      361 gccctgaaca gggatattgc gacaattcac agcaatatcg tacaggaata caacaccctt
      421 aaagggtata gctggaaatg gctgggtggg gtgtcagtgg cttttctggt tatgttctgt
      481 gtgctcggat ggggaatgaa aacaatactc gacaggaact acaacgccac agcggcggtg
      541 tatcagaaag ttgtgacact ggaagataaa ctggtggaga aacctgtcac ggggaagagc
      601 cggaaaaact gacgcgcttc gcttgtccaa cgcctcacga cccgcgaaag gatttcgcga
      661 accgttcacc gtttttttca atatgattct gtctgctttg gtcgataaag cagacgatag
      721 tattccagcc ttcgtatata taacggtacg tgctcatcag taagagctgg cggtattgtg
      781 ttatcagggg gaagtttttt cagatactca cgaaatgcct ggcttgatgc cataaaatct
      841 acagtagcat cgataatatg tggggtgttt tcacctaatt ttgccatgat gataatcctt
      901 atattatcac ggtttgtgaa tgatagggtg tcactattat ttatgcgtta gtgaaccaga
      961 aaaaatcccc cgttggcata gggggatatg taaggagaaa taacttcgca ggtgttcttg
     1021 tttgtataac gtgaaaagac tgcacgcaac ttaataagtc tgccgtactt actttcagtt
     1081 ttcaacataa ggtttataac aatgtatgga atggaagtga gctttaaggt ttcagctcta
     1141 aaaaataaaa tatttattag ttggctggtt gttgttcttg ttctgtatgt atataaacac
     1201 tatcgacata ttatgaccgg gaacattcct taccccctct gcgctcgcag aggttttttt
     1261 tgtcattaat taataatgaa ctgaaatgca gttccgatac ctccatttgc acattatccc
     1321 tgacatatgg taccggaacc gcattaattt tatgttataa gagtttattt ttaatgtcca
     1381 gatggtttaa tagtatttat atgtaattag ctgtatggat agtactggtt ttattgtata
     1441 acttgtcgtt ttttttattg tttttgtgtg gtgtgctaat ctttaagtta taaaaaaacc
     1501 ccttggaata caggggcaaa agtaaggaaa acaaatggat gctcagtttg tgtgacactt
     1561 taaactaatg gaactataga gtggaggttg ttacagtcgc ttttataaaa cagcaaccag
     1621 ttttttttca atagtctgat gatggttgtg acagttttgt gatattgttc aaaatgtttc
     1681 ttgttgaatg tttgtttttt ggtctattgg tgtctggttt tattttttct gctattacat
     1741 atcaagaaat gtgattggtg tagcaagagt ggaatgcgat gtggataaac taattggttg
     1801 tcgaatctaa tttacttaga aaactacact tgtttttgtg tatgaattta gtgaatttgt
     1861 ctgtctatgt gttttcgtgc atttataaat ccttcgtcag gatcttaaat ttagtgttga
     1921 atatgtaggg cctgtacggt aattattatt tagcgtagct acttcatcgt tgttcgaaca
     1981 caaccaacaa cctgtaattg ttgtttctct tggttcccca cttttgtggg gttttttatc
     2041 tcttccgtgc atcgtaaagc gcggactcct tctggaaagg ttgttttagg gcatcactga
     2101 ggcatttttt gcgtttgtga atattgagca tccgataact aaaatatttc ccatagactc
     2161 tgattcttgc caccgacccc aggtcggttt ttttttgtcc tggcgagatg tgaagtttgg
     2221 aaacaggaaa ccccgtcaga gcgccacgca ccaggggaga aaacttgtcg ttttgagccg
     2281 ttcggtgttc agaacgcacg aaaccgatcg cgggtcgctt tcgtgcatag ttatgcagcc
     2341 atctaaaaac gattctggcg cgtttttctg gtttagcctg gtgttttctt gtctttttgc
     2401 gttttttgcg ccagaaagcg attgagggcg ttttacaggg tacgtacaac gggagttatg
     2461 gtaaatggat cgggttttcg ggaaggttcg acaggatttg ccgttgggtg tagtgtaagc
     2521 gactgaaaaa caaacgcccc tgaaatcatg tccagatccg gcaagattca acatgaaata
     2581 cagagggcgt gtaggtcgca taacccggag agaatcgtaa cacatgagcg ccgcgcttca
     2641 atacttcgac gaaaatttac cccatcgtcc ctatcacacg gatgatctcg cttttggtct
     2701 tcgcatctcc ggcaaagggc gtgcgcttct tgcgcggtac atacagcaga accagcctca
     2761 tgcgcagttc tggctggttt ttgacgttga ccgcgagggg gctgcgattg actggagcga
     2821 ccggaacgct cccgcgccga acatcaccgt taaaaatcct gtgaacggac acgctcacct
     2881 gctctacgca ctcaacatcg ccgtgagaac cgcgcctgat gcctcggtta aggcgctgaa
     2941 atatgccgca gcggttgaac gttcgctgtg tgagaaactt tgtgcggatg tgaactacag
     3001 cggcctgatt tgcaaaaatc cgttccacct ggaatggctg gtgatggagt ggcgcgagga
     3061 agcctatacc ctcgatgaac tggctgatta tctcgatttg agcgcctcag agcgtcgtag
     3121 catcgataaa cattacggga tggggcgaaa ctgccacctg ttcgaaatga cgcgcaaatg
     3181 ggcttacagg gcgattcgtc agggctggcc agcgttctca cagtggcttg aagcggtgat
     3241 ccagcgtgtc gaaatgtaca atgcatcgct tcccgttccg ctttcactgg ctgaatgtcg
     3301 ggctattggc aagagcattg cgaaatacac gcacaggaac ttcacgccgg aaactttcgc
     3361 acagtatgtg gctgatacgc acacgccaga aattcaggct gcacgcggtc gcaagggcgg
     3421 ttctaagtct aagcgcagca cagtagctac atctgcacgc acgctgaaac cgtgggaggc
     3481 attagggatc agtcgcgcct ggtattacca actgaaaaaa cgaggtctcg tagagtagac
     3541 caaataagcc tatatcagat aacagcgcct ttctggcgtc tttttgagca gcaggttttt
     3601 tgccgttttt ccccgttcag ccctgcaatg gcgcggcttt ccgcgtgatt gtggtggtag
     3661 tgctcgccgc agtctcatga ccgagcgtag cgagcgaatg agcgaggaag caccagggaa
     3721 tcggaacacg gatggaggca cttacgcgtc tgggtttggg gatgtctcca gatcgtactt
     3781 aagttcctta agtgcctgta atatcctgtc ttttttatag catagctcgc ctgtttttgt
     3841 gtctagcagt cctgcttcga tcagtagccc agccgcgaga aagagccggt gattgcgttc
     3901 ccgtcgttgt ttttttccct cgattcgttt ctggaccgcc tgttttcgtt cgctctcctg
     3961 tgcctgtaag tcgttttttt ccgctgttgc cagtacgtgg aggagtttgc gttcctgttc
     4021 tgtgagtcct gcttcgttgt cgagcaggtc aataatctgt ctctgtcgtg cggtctgttc
     4081 tccgagcttc ctgatgaatc cgatccgttt cttcagccat tcgatgttgc tgatgcgcat
     4141 gttcgtggtg ctccctggtg ttttttgcgg tgtgttgtgg tcgtgcagta tatcgcttgc
     4201 ggtcggtggg tgcagggggg tatcttccgt gctaattcta aaaattagaa ggaagcgcac
     4261 ttatatgttt ctctccttcg tcgagaaaca gtgcgctcct gcggagggct gaaaccgtgg
     4321 caacctatca cctcagcgtt aaatttggtg gcaaggggca ggctgcaaac cacgccgatt
     4381 acatcgagcg caaagagaaa taccgcgacc gtcaggattt ggaatattcc gcacacggaa
     4441 acatgccgga atgggccagg gataatcctt cccatttctg gcaggcggct gaccagtttg
     4501 aacgtgcgaa cggttcgacc tatagggaac ttgaaattgc attaccccgt gaactgacac
     4561 cggaacagcg ccttgaactg gtgcaggatt ttgtacgtca ggaagctggc gaacggcacg
     4621 cctggagttt tgccattcac aatccgaaag cgagcattga cggcggcgaa cagcctcatg
     4681 cgcatatcat gatgagtcag cgtgtgaatg atggcattga acgtacaccg gaacagtatt
     4741 tccggcgcta taacgccagg tatcccgacc ggggaggtgc gaaaaaggat tccggaaacc
     4801 tgacccccac tcagcaaaaa gagcagttgc gggaattgcg aaaacgctgg gaggtgaagc
     4861 acaacgaaca tatgagaaag catggctttg aaaggggctt cattgactgc cggacgctga
     4921 aagaacaggg cattgaacga cgtcccgaag tgcatctggg ttttgaagct gctggacggc
     4981 ttgatgatgc ccagcgtcat gacatcatgc aaaaacggtc tgaaccggac tattcccgcc
     5041 atcttgaaca ggcgcgaacg gtcgggcatg acatcaggga atggctggac actccggtta
     5101 agcaacatga actggtcaga aggcttcaac atgatgttgc gcgggagcat ggctttgaca
     5161 tgagaga
//
