LOCUS       NZ_CP054359             4110 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-172 plasmid pSCU-172-6, complete
            sequence.
ACCESSION   NZ_CP054359
VERSION     NZ_CP054359.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943545
            Assembly: GCF_013315695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4110)
  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  JOURNAL   Unpublished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 4110)
  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                   :: 78x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:55:40
            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)                     :: 5,461
            CDSs (total)                      :: 5,339
            Genes (coding)                    :: 5,056
            CDSs (with protein)               :: 5,056
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 85 of 283
            Pseudo Genes (incomplete)         :: 198 of 283
            Pseudo Genes (internal stop)      :: 39 of 283
            Pseudo Genes (multiple problems)  :: 33 of 283
            Pseudo Genes (short protein)      :: 3 of 283
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054359.1.
            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..4110
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-172"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-172-6"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(9..131)
                     /locus_tag="HPE50_RS27660"
     CDS             complement(9..131)
                     /locus_tag="HPE50_RS27660"
                     /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_001329512.1"
                     /translation="MKNSKLQKSRTADTGKTLFNPVENQYSCGLNGYHQLSIGA"
                     /name="hypothetical protein"
     gene            448..1149
                     /locus_tag="HPE50_RS26930"
                     /old_locus_tag="HPE50_26940"
     CDS             448..1149
                     /locus_tag="HPE50_RS26930"
                     /old_locus_tag="HPE50_26940"
                     /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_000227989.1"
                     /translation="MVDLIAYKSNALVEASYKLTLQEQRFLLLCISRLQSGVDAPPPEL
                     QKTMTITAVEFFNSFPDMGRNHAEEKLQEAIDRLWDRSIILKDGEKREEFRWIQYRAQY
                     LKGEAKVQITFADAVMPYLTQLKGQFTKVVIKNISNLSKSYSIRIYEILQQFRNTGERM
                     ISLDDFRSMLQLEDKYKDFKTLNRALIKPAVAELNQKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1399..3558)
                     /gene="mobQ"
                     /locus_tag="HPE50_RS26935"
                     /old_locus_tag="HPE50_26945"
     CDS             complement(1399..3558)
                     /gene="mobQ"
                     /locus_tag="HPE50_RS26935"
                     /old_locus_tag="HPE50_26945"
                     /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_052940773.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILSPATAPAWCTNRTELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLSLEIQIFRTELRNSGLTEPARRVADLLNIELPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMTDMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTEFETQWQQWGASGLAALRAQL
                     LKREEELRRKELEDTERSRAERRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     SYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPEFFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNRHLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            3736..4026
                     /locus_tag="HPE50_RS26940"
                     /old_locus_tag="HPE50_26950"
     CDS             3736..4026
                     /locus_tag="HPE50_RS26940"
                     /old_locus_tag="HPE50_26950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000091756.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVSRIQPLIDELNALPKPVPKGVSKNGQQA"
                     /name="hypothetical protein"
     Typing          complement(3201..3559)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          3560..3735
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.382"
                     /coverage="100.0"
                     /evalue="9.6e-71"
     Typing          complement(1403..3645)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.791"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagggcactt acgcgccgat gctcagttgg tgatagccgt tcaacccgca tgaatactgg
       61 ttttccacag ggttgaacag cgttttgcca gtgtctgctg ttctgctttt ttgtaacttg
      121 ctgtttttca tgggtttttg ttttgcgcac cccgagtttt ccacaggctc gccgttaagt
      181 ttttagatct tgtttttaag atcttgtttt taatacttgt tttcggaccg aaatttctta
      241 tggaattcaa gggattagat tgctataggt gaacatttcg ggggtaaagg tgaacatttc
      301 gggggtggtt aggtgaacat ttcgggggta aaggtgaaca tttcgggggt ggttatccac
      361 agaaaatggt gaattaaaaa aaaatgattg caccaattga tggggtgaac tagttttttt
      421 ttagtttact ttaggtgagg gtgctcaatg gttgatttga tagcttacaa atccaatgcc
      481 ttagtcgaag ccagctacaa gctcacgtta caggagcagc gtttcctgtt gctgtgcatt
      541 agtcgattac agtcaggtgt tgatgctcct ccacctgaat tacaaaagac catgactatt
      601 acggctgtgg agttttttaa ttcatttcct gacatgggaa gaaaccatgc cgaagaaaag
      661 ttacaggaag cgatcgatcg tctgtgggac aggtcgatca ttcttaagga tggtgaaaaa
      721 cgcgaggagt tccgttggat ccagtatcgg gcgcagtacc tgaaaggcga agcaaaagtt
      781 caaataactt tcgcagatgc tgtaatgccg tacttaacgc aattaaaagg gcaattcaca
      841 aaagttgtaa ttaaaaacat atctaattta tcaaagagtt atagcatcag aatatacgaa
      901 atcctccaac agttccgtaa cacaggggag cggatgattt ctctagatga tttccgcagc
      961 atgctacaac tggaagataa atataaagat ttcaagacgt taaatagagc cctcataaaa
     1021 ccggcagtgg cggaactgaa tcaaaaaagc gatctggccg taacggttga gacaatcaag
     1081 aaggggcgca ctgtcgtagc cctgcatttt cgcttcaagg aagacaaaca gatcaagatg
     1141 acgatctaaa atcgattcta aggcatctaa aacgcgcgct gacgcgtttt ttttgtgtaa
     1201 ggtatgcgat ggtactacga atcacaaaaa catcgtcaga atcgctctca cgagctaaaa
     1261 aaatccccca tatgcggggg gaagaaacta tgcggagatt atctagtttg ttgtgtgtgc
     1321 ttattgacgt tcatccctgt catgtgaacg tcacatgaac ataacatgat gttaaacaaa
     1381 acaaaatatt gtgcacattc actgtgacca accgcgatcg tgcctcctct cggtggcgtg
     1441 tgttcgtgca tcttcctcgc gccgccattc gtcccaggta cgattaaaac ccagcgagcg
     1501 gaacagatga tccggctgtt tttctggtgt attgacggca gcaaaaagcg gtgcctcacg
     1561 ggttttcaga tgaaactcca taagttccgg tgcaggtgat atgtggctgt ctgcatcgtg
     1621 attgacggca acaccatacc ctgcataccg taaccccttg tccgtcagcg cactgatgac
     1681 cagatgcctg ttatcggctg agggaacggc aaacgcggga tacagcgtgc cattaagccg
     1741 gacaacgccg cccagagagt catccacgcc catgaccagc aaaagctgaa gctggcgggt
     1801 ttcccggtcg acagaactca ttaccggcat cagcgtcggt ggcagacgtc cctgcgtaaa
     1861 atccaccttc cttgctgcca gtgatggcat ggctggctgg cggtcttctc caagacagaa
     1921 aaactccggc catgtcttcg gctggcggag attgcgggta tgttgtggcc atgtctggca
     1981 aacctgcgtc agcagttgct caaaggtcgc agaggaataa acacgttgca gtggtggatg
     2041 ttgaccgatt tcgcttcggt cacagatata accactcctg tcacgcatta aatcaacacg
     2101 ctcaaagatt ctggtgcggt atttctccag ctcgttcccc cagagcgtat attctccgtt
     2161 ccggttgtga agcagaaggt aactggtcat ttccccgtta ccaggcatgg gggcctcgcc
     2221 ataccccgta acgactgctc tcagtacccc tgaatccata acggcattgt catttttcct
     2281 gagctgctcc gctcgtcgct ccgcgcgact acgttctgta tcctccagct ccttccggcg
     2341 caattcctct tcacgtttaa gcaactgggc tctgagagct gcaaggccgg atgcccccca
     2401 ctgctgccac tgtgtttcaa attccgtctg actcgcggga atgtcctgtt tctccacctt
     2461 ccggtaatgc tgtcgcaatt tttccatttg ctggctcaga gactgaattt ttccctgctc
     2521 actacggtat tccggtgcag cccattgcat caggggaata cgggaaaaac cggacgaaaa
     2581 cggcgatgat tttttcaggc tggcagcatg gctcatcgct tcctttcgtt cggtgttcag
     2641 ctcttcccag cgtctgcgcg tcgcctgcat atctgtcatc atcgacatgg cattactggt
     2701 gagtttccat gccgcgttac tgtccttcgg caacgcttcg atgatgtcac gtagtgtgta
     2761 cgaagttgcg ttgtcaggaa gctcaatatt cagaaggtca gccacacggc gggcaggctc
     2821 tgtcagcccg ctgttcctga gttcggtacg gaaaatctgt atttccaggc taagcctgtt
     2881 aatcagacga ttctgttcgc cgcgttctgt ttcgataccg cgtgtttcca tcgcacaggc
     2941 agactttccg aggtgaatac caggcgtttt ctcaagcccc tgtcgctcgt atgaacgatg
     3001 gtctatctct tcctgataac cggcgttcgc cagtgccctg tttgcatggt cagcccatga
     3061 tgcccgccac gtctcggcat gtgtccggtc gttccagtcc ctgacctttc caccgaaccc
     3121 cgcaggtccg acagccctcg tggtcagcat gatgtgcgca tggggatttg ttttatccat
     3181 gtgatggaac gccacatcag caatcatgcc ctgactgaca aagttttctc tgacaaaggc
     3241 gagaacggtt tcccgtgcgg catcctgcgg cagttcacgg gggatggcga gttcaatttc
     3301 ccgcgcaagt tgtgagttct tccgacgttc ggccttctca acggcattcc agagttcggt
     3361 acggttcgta caccaggcag gggcggtggc gggggacaga atcacagcct cagccacacc
     3421 gcttttgcgg gtgtagtcgt gagtcagtcc ggtacgctca tcaagcatta gtgaaccgga
     3481 acgataggca gcagaagcaa cggcgctgta gccgttgctt ctggagatga ttttcatgct
     3541 gagatgataa atcgccattt ctgccgtaat gcctttttgc agttttcttt cagccccgca
     3601 gggcgcacac aatcgaaccg aaggtgagat tgtataagtg cgcacttcgt gatttctgcg
     3661 cattatgcca gctcagtttt taaactacca gtgacgagct aaaatgcgat ttttcaccgc
     3721 gcacggagtt acatcatgag cagaacactc gaacagaaaa ttgccgaagc tgaagccaga
     3781 ttgcagcgtc tgaaggcaaa gagccggagc ctggacacag cgcagaaggt cgttgtaggt
     3841 gctgcattgc tggcaaaggt cagaaagccg gaggaggtgc aattgcgcgc ctggttactc
     3901 cagttcctga aggcagaggt gacacggcag gctgatgtga gcaggataca gccgttgatt
     3961 gacgaactga acgcgttgcc aaaacccgtc cccaaaggcg tgtcaaaaaa cggccagcag
     4021 gcgtgaatgc accatccgct cgccgcagcc ccagcgaccg agcgttagcg agcgagtggg
     4081 cgaggaagcg gaaaagctgc tgcaccaaaa
//
