LOCUS       NZ_CP049104             6126 bp    DNA     circular CON 12-JUN-2023
DEFINITION  Escherichia coli strain EC28 plasmid p4, complete sequence.
ACCESSION   NZ_CP049104
VERSION     NZ_CP049104.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14149865
            Assembly: GCF_011044355.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6126)
  AUTHORS   He,F.
  TITLE     Genomic and phylogenetic analysis ESBL-producing Escherichia coli
            ST429 strain isolated from a urinary tract infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6126)
  AUTHORS   He,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-FEB-2020) Department of Clinical Laboratory, Zhejiang
            Provincial People's Hospital, 158 Shangtang Road, Hangzhou, Zhejiang
            310014, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 250.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/12/2023 02:51:02
            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)                     :: 5,169
            CDSs (total)                      :: 5,056
            Genes (coding)                    :: 4,878
            CDSs (with protein)               :: 4,878
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 65 of 178
            Pseudo Genes (incomplete)         :: 121 of 178
            Pseudo Genes (internal stop)      :: 32 of 178
            Pseudo Genes (multiple problems)  :: 36 of 178
            Pseudo Genes (short protein)      :: 4 of 178
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP049104.1.
            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..6126
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC28"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4"
                     /geo_loc_name="China:Hangzhou"
                     /collection_date="2018-06-03"
                     /collected_by="Fang He"
     gene            464..613
                     /locus_tag="G5V60_RS25595"
     CDS             464..613
                     /locus_tag="G5V60_RS25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_164699461.1"
                     /translation="MPSEYDEQRDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            1082..1273
                     /locus_tag="G5V60_RS25600"
                     /old_locus_tag="G5V60_25565"
     CDS             1082..1273
                     /locus_tag="G5V60_RS25600"
                     /old_locus_tag="G5V60_25565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1273..1674
                     /locus_tag="G5V60_RS25605"
                     /old_locus_tag="G5V60_25570"
     CDS             1273..1674
                     /locus_tag="G5V60_RS25605"
                     /old_locus_tag="G5V60_25570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-binding protein"
                     /protein_id="WP_087775217.1"
                     /translation="MARVSISEASRLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="DNA-binding protein"
     gene            2266..3261
                     /locus_tag="G5V60_RS25610"
                     /old_locus_tag="G5V60_25575"
     CDS             2266..3261
                     /locus_tag="G5V60_RS25610"
                     /old_locus_tag="G5V60_25575"
                     /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_087775211.1"
                     /translation="MKFFLKKSVVLGSSAIGITLLFIACFLSIQFGRYISPSDRISLTG
                     KTELENKLDEYMNDSYINEATNKVSELSGKLIMQGGNAASPESIQETKVKTEVLSKDKD
                     LDYNSYDSEFLGKKRVITYINLLSVEDSIYKILYPNVDCLGKTFSGTFEGDKPKSKKEC
                     ESEVIKIHKKDAENQRNTIAKIKEINDFIAGKIKPLKDEVIANGGAVKLWMPGPSIDTC
                     SEHTAMASEDIPEAYKTKNECISAINKKIKDIDEENARNEGMISFFPFIVILVAILLMP
                     AALKISSLIIKAALNLWLVFLEKSSESINKSEKKIKIDAKIEMREKKDKE"
                     /name="hypothetical protein"
     gene            complement(3366..3590)
                     /locus_tag="G5V60_RS25615"
                     /old_locus_tag="G5V60_25580"
     CDS             complement(3366..3590)
                     /locus_tag="G5V60_RS25615"
                     /old_locus_tag="G5V60_25580"
                     /inference="COORDINATES: protein motif:HMM:NF020291.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="primase C-terminal domain-containing protein"
                     /protein_id="WP_235891633.1"
                     /translation="MQACYERASAYNLQFAPPLDENEVDGIAKSIAKWTISKFSEDQFM
                     DFVKATHTPEIQSKRGKKGGVKSRRAVGK"
                     /name="primase C-terminal domain-containing protein"
     gene            4149..4979
                     /locus_tag="G5V60_RS25620"
                     /old_locus_tag="G5V60_25585"
     CDS             4149..4979
                     /locus_tag="G5V60_RS25620"
                     /old_locus_tag="G5V60_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001694615.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047667779.1"
                     /translation="MAVTDVDFELKIESGANLVDMEYGLETMTGFSGAIAITADCILSN
                     EVPSKMSYSDNVRAKLMGACLGSYKQDFKLVISDPVKSANLERIGNSVLSELITYFICE
                     TMYVEPPALTKKAEKILSKMEKIESKVIDRIYERVKDMHKISRSNKYPVVLKRKTQLRN
                     FKLFEINENTASNLFNLTTDNNSVEIDAIVTRFNSFTGNGRLLADGDSVTIPFSFSGPY
                     SKVKASTKRLMSENLHDNNAVADELITRLKITANAKRNTSGDIVKYMILSADKP"
                     /name="hypothetical protein"
     gene            4976..5704
                     /locus_tag="G5V60_RS25625"
                     /old_locus_tag="G5V60_25590"
     CDS             4976..5704
                     /locus_tag="G5V60_RS25625"
                     /old_locus_tag="G5V60_25590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001694614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_087775214.1"
                     /translation="MSNRLWLVVFILALLAFCGVFIVYFLWFKAWLNFHLSKNPEVWGQ
                     FGDFVGGVLNPILSFITVVILIITTIYQQKQYENSEKRELNKRFDDRFYGMISYQRDLV
                     ANFKLALPGNSDAGVKDAITYAEDVFFNTNDHSYINSQGFKEAIFPVVRTFYILIKMID
                     ESSEDEVSENIASKYYEWLVNLSDYHFLRLVFFCSFYYDGISSFDYIKSNKNIVSSLAK
                     MGWDKYTSEIIQRKHQLSIA"
                     /name="hypothetical protein"
     Typing          complement(2..132)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.939"
                     /coverage="90.0"
                     /evalue="1.17e-48"
     Typing          complement(5890..6126)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.816"
                     /coverage="87.0"
                     /evalue="3.88e-104"
ORIGIN
        1 gagccatcag ggggaaacgc ctgatatctt tatagtcctg tcgggtttcg ccaccactga
       61 tttgagcgtc agtttttgtg atgcttgtca ggggggcgga gcctatggaa aaagcgccgg
      121 tgcgcggcct ttttctcttc ttgcgcacat gccgcgtggc gctttatccc ctgaatctgt
      181 ggattcatca tgagcttgtt gtgtgagcgc aggtaacgcc cgccgcagcc gaacggcagg
      241 agcgtctgcg actgagtgag cgaggaggcg tcatatcccc gggcttccat tttctcccgt
      301 acgccccgcc gctgcacttt cctctgtcac atgaagcact ttcataacgt gttactccac
      361 cgtagcatat tgagcccgta cacactccgc tagtgctact tgactggttc agggctgcgc
      421 ctagaaaccc gctaacaacc tctcagctac tggatatcac cccatgccat ctgaatatga
      481 tgaacaacgg gattcgactg atacgcagct tcccggcgaa tatgaccttt ttgatttaat
      541 ggcgcaggtt actgaagaga acctgcacgc ccctgtggat tctgggccgc ctgtcggccg
      601 ggaagcgtta tagctttttc gcttgcccgc gtacgtggta atacgccggt attacatttt
      661 atttctttat tttcatgtga ttacaggtga ttgtaatacg ttgcgtatta cataaataaa
      721 cggagatttc agtttttacc ttttaattca tgcagttgcg atgaaaatcg cggctgcgtt
      781 aggtgtatga ccatttaagg ggcaaaaaat tatcattctg gccgcgttat ctgcgcaggt
      841 taaggagcac cggcgacgaa aaagcgtctt taactgcttc gttcatgctt gcatgaacgg
      901 attatttttc cggactacag gaagactaca aaagttgatg acttaatcct gatttttagt
      961 gcgatgacta cagataaact acaaaataac tacaggatta cctcagatcc gttctctgaa
     1021 ccatttgtac atccgacccc cttaccggtt tacactgagc actgatgctc tgagggccct
     1081 tatgacgaaa caacagaaaa cagcgctgaa catggctaaa ttcatccaga atcagtctct
     1141 gctcctgctg gagaagctta acgagcttga tctcgatgtc gaggccgacc tttgtgagaa
     1201 actccacgat gatgcggagc atcttttccg tacactgtcc tcgagactgg atgcattaca
     1261 ggatggtaac tgatggccag agtgtctatt agtgaggcgt cacgactgac gggtaagagt
     1321 agaacaacac tgcacaggtt aattaaagca ggtgacctgt ccacctgtag cggtgaacgt
     1381 aatgcaaaaa tggtagatac ttcagagctt ttacgtgtct ttggtccctt tgagcaaccg
     1441 aagggtgaac accattctgg acaggtctct gaacagcgtg atacagcctc tgctgaccag
     1501 agtgaacagg tgattcgtca tctgaaacag gagattgaac acctgaacac cttacttttg
     1561 tccaaggatt cgcacattga cagcctgaaa caggccatgc tccttcttga aaatcaccag
     1621 gcaaaattaa ctgaatcccc ggcgccatgg tggaaattct ggaaaaaatc ctgaccccgt
     1681 catgcttaag ttttcctctc cggtcattcc ggggagttcc tgaaccttcc caaaaatcgt
     1741 cagatctctg aacgctcctc actactaaaa atacccacac cccacgcaaa attaaaattt
     1801 tgaagataac tcattaatat cagttagttg tgggttatta aattacgcag tattactttc
     1861 tgtaaggtga atccaagtcg tcggcgattc gtgtacgact tgccgacgac tcgtcataga
     1921 gtcatcgacg actcacttaa gactatcagt aacttatgac gacttgactc tagagtcgaa
     1981 tcgtcatttt ggtgtttttt tgaccttggc gactctagag tcaagtcacg agtcgaatcg
     2041 ccggtgaatc gtgtggtgag tcgtccggcg acttgccata acgtgattgc cggccgtcga
     2101 cgaacccgat tcctgaacgt gctgaaaacc ggttgccggc gcagccggaa aaccggtttt
     2161 cagcacgttc aggaaggggg gcgatgtatg tataggcttg ttctggtcca cgcgatcaga
     2221 tgttaagatg gtttatcgtt tcccttctgt tggattcttc taaaaatgaa attttttcta
     2281 aagaaaagtg tcgttttagg ttcctcggca ataggtatta ctttgctatt tatagcttgt
     2341 tttttatcaa ttcaattcgg gaggtatatc tcaccctcag acagaattag tcttactggt
     2401 aagactgaat tagagaataa gttagatgag tacatgaacg acagttatat caatgaggca
     2461 acaaataaag ttagcgaatt atctggtaag ttaataatgc agggaggtaa cgctgcatca
     2521 ccagaaagca ttcaagagac aaaagttaaa acagaggttt tgtctaagga taaagatctt
     2581 gattacaaca gctatgattc agaattctta ggcaagaaga gagtgataac ttatataaac
     2641 ctattgtctg tggaagatag catttataag attctttatc cgaatgttga ttgcttaggt
     2701 aaaacatttt caggaacatt tgagggtgac aaaccaaaat caaaaaaaga atgtgagtct
     2761 gaagtaataa aaatacataa aaaagatgct gaaaaccaac gaaacactat cgctaaaatc
     2821 aaagaaatta atgattttat agctggtaag ataaaaccgc ttaaggacga ggtaatagca
     2881 aacggcggag ccgtaaaatt atggatgcct ggcccatcaa tcgacacctg ttcagagcac
     2941 actgcaatgg catctgaaga tatacctgaa gcatataaga caaaaaatga atgcatatcg
     3001 gcaattaata aaaaaataaa ggatattgac gaagaaaatg ccagaaacga aggtatgatt
     3061 agtttttttc cttttattgt aatccttgtg gcaatacttc tcatgcctgc tgcgttaaaa
     3121 atatcctcac taataatcaa agctgcacta aatctctggc ttgttttttt agagaaaagc
     3181 tcagaatcta taaataaatc tgagaagaaa ataaaaatag atgcaaagat agaaatgaga
     3241 gaaaaaaaag ataaagagta aagttgtcgg ggttagaagt taaagctccg acttcaactt
     3301 ataataaata cttctactta tccccatcga acaccacggt ttactttgtc tctcacttcg
     3361 tgggtttatt ttcctaccgc ccttcgactt ttcaccccgc ctttctttcc ccttttagat
     3421 tgaatttcag gagtatgggt ggctttcaca aaatccataa attgatcttc tgaaaatttt
     3481 gagatggtcc atttagcaat acttttcgct attccatcta cctcattttc atccagaggt
     3541 ggtgcaaatt gtaaattata ggcactggca cgttcatagc aggcttgcag ccattggtcg
     3601 tactcaagcc agccctgacg aattgtgcgg tatgcccact ttccggctgc accggcaacg
     3661 cttcacggcc acgcaataaa ttgcgtcccc gttcaccgtt ttcggatagg aagaacgccg
     3721 gaaacaggac ttaccccggc tgaatggcgt gaattttcgc gctatgcact tgcgtgcata
     3781 ctcatgcatg ccgtaaaaac agagcctgcg cgtttctggc gggttttcgg gtggtttgtt
     3841 gcctgtttta ccggtttccc gtcagaaacg ccctgaggcc gtttgggcgg tgcgtacaat
     3901 tagggggtta tgttaaatgg caggcgtaaa atgtcatgac gggacaaaga gtgtattaag
     3961 tgactgacat acagtgaatt tattgtggta aatcacatct atcagtggct atgtgatgct
     4021 aactttacta ccgattttta cggttacgtt tgttaagttc tggaaggtga gttattcaga
     4081 tagtattatc aaagtaatta acatttgctc ttaacttaat gaattgaatg gatttataag
     4141 gaacttcaat ggcggtcact gatgtggatt tcgagctaaa gatagagtct ggagctaact
     4201 tggttgatat ggagtatggc ttggaaacca tgacggggtt ctcaggtgcc attgctatta
     4261 ccgctgattg tattttgtct aatgaagtac catcaaaaat gagctactct gataatgtta
     4321 gggcaaagct aatgggggct tgtcttgggt catataagca agattttaag ctggttattt
     4381 cagaccctgt taaaagtgct aacctagaaa gaataggtaa ctctgtttta tctgagttaa
     4441 taacgtactt tatttgtgaa accatgtatg ttgaaccccc agctttaacc aagaaggctg
     4501 aaaaaatatt atctaaaatg gagaaaatag aaagtaaagt aatagatagg atttatgagc
     4561 gagtgaaaga tatgcataaa atttcccgtt ctaataaata tcctgttgtt ttgaaaagaa
     4621 aaacgcaatt aaggaatttt aagcttttcg agataaatga aaatactgca agtaaccttt
     4681 ttaatctaac tacggataat aactccgttg aaatagatgc gatcgttaca agatttaatt
     4741 ccttcacagg gaatgggcga cttcttgctg atggtgattc agttactata ccatttagtt
     4801 tttctggtcc ttatagtaaa gtgaaggcgt caacaaagag gcttatgtcc gagaatcttc
     4861 atgacaacaa cgctgttgct gatgagttaa taacgagatt aaaaataaca gcaaatgcta
     4921 agcgtaatac atcaggggat atagttaagt atatgatatt gagtgcggat aagccatgag
     4981 taatcgcttg tggttagttg tttttatact ggctttgctg gccttttgcg gtgtttttat
     5041 tgtatatttt ttatggttta aagcttggct taattttcac ttatctaaaa atcctgaagt
     5101 atgggggcaa ttcggtgatt ttgttggtgg tgtattaaat ccgatactca gttttatcac
     5161 tgttgttata ttgataatca ccaccattta ccagcaaaaa cagtatgaga actcagaaaa
     5221 aagagaacta aataaaaggt ttgatgatag attttatggg atgatctctt accagagaga
     5281 tttggtggca aattttaaac tcgctttacc tgggaactct gatgcaggtg tgaaagatgc
     5341 cattacttat gccgaagatg ttttttttaa tactaatgac cattcttata ttaattctca
     5401 agggtttaag gaagccatct ttccggttgt aagaacattt tacatcttga tcaaaatgat
     5461 tgatgaatca tccgaggatg aagtgagtga aaatattgca tcaaagtatt acgagtggtt
     5521 ggttaacttg tctgattatc attttttgag gctcgttttc ttttgctctt tttattatga
     5581 tggtatatct tcattcgatt atataaagtc gaataaaaac attgttagta gtttggcaaa
     5641 aatggggtgg gacaaataca catctgaaat aattcaaaga aagcatcagc taagtattgc
     5701 ttgatgctct cgtaggatgt atcgtctggc taaacgaaaa aaccgccttg gcgggcggtt
     5761 ttttcgaagg ttcatggagt tggcgctcgt tgaaccgagg taactggctt ggaggagcgc
     5821 agtcaccaaa acttgttctt tcagtttagc cttaactggc gcacaacttc aagactaact
     5881 cctctaaatc agttaccagt ggctgctgcc agtggcgttt ttcgtgtctt tccgggttgg
     5941 actcaagatg atagttaccg gttaaggcgc agcggtcgga ctgaacgggg ggttcgtgca
     6001 tacagtccag cttggagcga actgccttcc cggaactgag tgtcaggcgt ggaatgagac
     6061 aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa tggcaggaac aggagagcgc
     6121 acgagg
//
