LOCUS       NZ_CP054162             6222 bp    DNA     circular CON 10-DEC-2023
DEFINITION  Escherichia coli strain STO_Bone2 plasmid pBone2_2, complete
            sequence.
ACCESSION   NZ_CP054162
VERSION     NZ_CP054162.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15006795
            Assembly: GCF_021498145.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6222)
  AUTHORS   Li,F., Luthje,P., Shafeeq,S., Ahl,M., Akerlund,B. and Romling,U.
  TITLE     Characterization of Escherichia coli isolates from a chronic bone
            infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6222)
  AUTHORS   Li,F., Luthje,P., Shafeeq,S. and Romling,U.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAY-2020) Department of Microbiology, Tumor and Cell
            Biology, Karolinska Institutet, Solna vagen 9, Stockholm 17165,
            Sweden
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 1043x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/10/2023 02:37:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,145
            CDSs (total)                      :: 5,018
            Genes (coding)                    :: 4,804
            CDSs (with protein)               :: 4,804
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 82 of 214
            Pseudo Genes (incomplete)         :: 133 of 214
            Pseudo Genes (internal stop)      :: 52 of 214
            Pseudo Genes (multiple problems)  :: 47 of 214
            Pseudo Genes (short protein)      :: 4 of 214
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054162.1.
            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..6222
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STO_Bone2"
                     /isolation_source="bone infection of foot"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBone2_2"
                     /geo_loc_name="Sweden: Stockholm"
                     /lat_lon="59.351331 N 18.026000 E"
                     /collection_date="2005-01-01"
                     /collected_by="Karolinska University Hospital"
     gene            join(6158..6222,1..>340)
                     /locus_tag="HRS05_RS25150"
                     /old_locus_tag="HRS05_25030"
                     /pseudo=""
     CDS             join(6158..6222,1..>340)
                     /locus_tag="HRS05_RS25150"
                     /old_locus_tag="HRS05_25030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(447..1283)
                     /locus_tag="HRS05_RS25155"
                     /old_locus_tag="HRS05_25035"
     CDS             complement(447..1283)
                     /locus_tag="HRS05_RS25155"
                     /old_locus_tag="HRS05_25035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(1283..2086)
                     /gene="aph(3'')-Ib"
                     /locus_tag="HRS05_RS25160"
                     /old_locus_tag="HRS05_25040"
     ARG             complement(1287..2086)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(2147..2962)
                     /gene="sul2"
                     /locus_tag="HRS05_RS25165"
                     /old_locus_tag="HRS05_25045"
     ARG             complement(2151..2962)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(3422..3580)
                     /locus_tag="HRS05_RS25760"
     CDS             complement(3422..3580)
                     /locus_tag="HRS05_RS25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            4151..4300
                     /locus_tag="HRS05_RS25170"
                     /old_locus_tag="HRS05_25050"
     CDS             4151..4300
                     /locus_tag="HRS05_RS25170"
                     /old_locus_tag="HRS05_25050"
                     /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_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(5067..5507)
                     /locus_tag="HRS05_RS25175"
                     /old_locus_tag="HRS05_25055"
     CDS             complement(5067..5507)
                     /locus_tag="HRS05_RS25175"
                     /old_locus_tag="HRS05_25055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            5725..6114
                     /locus_tag="HRS05_RS25180"
                     /old_locus_tag="HRS05_25060"
     CDS             5725..6114
                     /locus_tag="HRS05_RS25180"
                     /old_locus_tag="HRS05_25060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     ARG             complement(451..1283)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          3943..4116
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(3414..4019)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acccgagcaa acccttctct atcagatcgt tgacgagtat tacccggcat tcgctgcgct
       61 tatggcagag cagggaaagg aattgccggg ctatgtgcaa cgggaatttg aagaatttct
      121 ccaatgcggg cggctggagc atggctttct acgggttcgc tgcgagtctt gccacgccga
      181 gcacctggtc gctttcagct gtaagcgtcg cggtttctgc ccgagctgtg gggcgcggcg
      241 gatggccgaa agtgccgcct tgctggttga tgaagtactg cctgaacaac ccatgcgtca
      301 gtgggtgttg agcttcccgt ttcagctgcg tttcctgttt ggggtcgttt gcgggaaggg
      361 gcggaatcct acgctaaggc tttggccagc gatattctcc ggtgagattg atgtgttccc
      421 aggggatagg agaagtcgct tgatatctag tatgacgtct gtcgcacctg cttgatcgcg
      481 gccgcgatag ctagatcgcg ttgctcctct tctccatccg cgttccaagc tgcggaaagg
      541 cacccataag cgtacgcctg gtcgagcagg cgacgcggat cgacgtccag cgcacgagag
      601 aatgcgtccg ccatctgtgc aatgcgtcta ggatcgagac aaaggtcgtc tctgtcagcc
      661 ggatcgtaga acatattggc ggcgccaaag cccacttcac cgaccagacc gacgggatct
      721 atcaccagcc agccgcgact ggagaacatg atgttttcat gatgcagatc gccatgtagc
      781 ccacgcagtt ccgaggcatt gctcatcatt tgatcggcta taatcgccgc gtggacgtag
      841 tcagtttgac aacctgcgtt ttgatcatcg cgcgcccgct gaaacaaagc tgcaaagcga
      901 tcccggatcg ggagaagggc agaaggcagg ggttcctcag atgcggcata cagcttcgcc
      961 attagttccg ctgcaatttc ggtcgcctgg tagtcgccgt gctcggcaac gatgtgagag
     1021 agcattcgct ccccggcata ttcgagcaac atcagattgt tctcacgacc gagcaaccgg
     1081 actgctcccc tcccattgcg ccataccaga tagtcggccc cgcgcagttc atcagcaatg
     1141 tcttctatag gtttcaatcc cttgacgatt gcaggagtcc cgtctggcaa tgaaactttc
     1201 caaacgaggc tggaaaaggt gtccgcaatg agaacaggtt gcgaaacgtg ccaatgagca
     1261 ggaaaaacag gcggcatgaa catcaacccc aagtcagagg gtccaatcgc agatagaagg
     1321 caaggcgttc gcggtcgggg gcttcgatcc ccaatacatt gaataggaca gcgaaggcgc
     1381 gctctgcttc atctggcgct gcccagttct cttcggcgtt agcaatcatg agtgccaaat
     1441 cggcatagcg atctgctgtt ccgagccgcc caaggtcgat cagacccgtg cattgaagag
     1501 ttttagggtc caccatgaag ttcggcatgc agggatcacc atggcaaaca accatatcgg
     1561 tgcgctcttg gtcgagccgc accggtagct ctcgttcgac acgagccaaa agatcgagct
     1621 gcggcgtact cttgtcctcg tccggtaaga agtcgggatt gacggcattg cgggacacca
     1681 catcaacggc gcgtccgaac attcgcgaca gcctgcgctc aaacggacat tgatcaaccg
     1741 ataggctgtg aacagcgcca agttgctgcc ccattgacgg ccacgctttg agcaaatccg
     1801 ctccagacag atcagccgcc ggtactcccg gaattgccgt tatcaccaag catgcaccct
     1861 cctgttcctc ctgccagttg atgacctcgg ggcaagccac acctcgacct ttgagccaaa
     1921 tgaggcggtc acgctctcca gcgagctcac cgcggcggga agcaggtgcg attttcgcga
     1981 aggcatgccc gtcaccacgt cgaaaaacaa aatcaccaga ttctccgcct ctgacaggca
     2041 accagtcaga atgcgattca ccaaaaaaaa tattagttcg attcaatgga ggttccttca
     2101 gttttctgat gaagcgcgaa tatagagaaa tatcccgaat gtgcagttaa cgaattcttg
     2161 cggtttcttt cagcgccgcc aataccgcca gcccgtcgcg caaggggcgc ggctcgtgtg
     2221 tgcggatgaa gtcagctcca cctgcggcgg cggcaagctc tgcagcgagt gtcgcggccc
     2281 cgacatcccc cggaccacgg cctgtgagcg cgcgcagaaa ggatttgcgc gaaacagaca
     2341 gaagcaccgg caaatcgaag cgcagccgca attcatcgaa ccgcgccagc accgagagcg
     2401 aggtttcggg agcagccccc agaaaaaacc ccatgccggg atcaaggaca aggcggttgc
     2461 gtttgatacc ggcacccgtc agcgccgcga tgcgcgcgtc aaagaacgcc gcaatgtgat
     2521 ccatgatgtc gccagcgggt gcctcgcgcc gatctgcctg cccgtcttgc accgaatgca
     2581 taacgacgag tttggcagat gatttcgcca attgcggata gaacgcagcg tctggaaaac
     2641 cgcgaatatc attgagatag gccacaccac gcgacaaggc ataggcttgc gtcgcgggtt
     2701 gataactgtc gagcgagacg ggaatgccat ctgccttgag cgcgtccagc accggcgcga
     2761 tacgcgcgat ttctgtgtcg gacgaaacag gcgcggcgtc gggattgctg gatgccggac
     2821 cgaggtcgat cacatctgcc ccctcggcca tcagcttacg cgcctgcgca atggctgcgt
     2881 ctggcgccag ataccggcct ccatcggaga aactgtccga ggttatgttg acgatgccga
     2941 aaatgatgag cgatttattc atgggggctt ctataataat aataatcgag catgagtctc
     3001 atacggatgc tcgggtcgaa agggaatccc caggcgagta acctgtttgc ggtgatccgt
     3061 ttcatgatga tgtatctgta gcattttgga aataaatata tcatctctca ataagtagat
     3121 atatttatct tttttgcttc tttggtgctg caagtcacca atacgaggga aacctgttac
     3181 ggagcggttt aaccgtaatc aacagtgact ggtgtcatgt tcggaagatt aattgatagt
     3241 aatctacaaa ggatcttctt gagatccttt tcaatgaatc gtaatctctt gctctgtaaa
     3301 cgaaaaaacc gcctggggag gcggtttgtt cgaaggttaa gtcagttggg gaactgctta
     3361 acccggtaac agggttcacg agaccgccat taccaaaact gttctttcag tgtagccgca
     3421 gtcaggcctc tacttcaaga cctcttaatc tatcttctcg tgcactcctg ttactaatgg
     3481 ctgctgccag tggcgttttg tcgtgtcttt ccgggttgga ctcaagttga tagttaccgg
     3541 acaaggcgca gcggtcggac tgaacggggg gttcgtgcat acagtccagc ttggagcgaa
     3601 ctgccttcac ggaactgagt gtcaggcgtg gaatgagaaa ccgcggccat aacagcggaa
     3661 tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcta ccagggggaa
     3721 acgcctggga tctttatagt cctgtcgggt ttcgccacca ctgatttgag cgtcagattt
     3781 tgcgatgctt gtcagggggg cggagcctat ggaaaaacgg cttcgccgtg gccttatctc
     3841 ttctttgcta agtgtcttcc tggtatcttc caggaaattt ccgtccccgt ccgtaagccg
     3901 gtaccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaat
     3961 atctcctgta tcgcatattc tgctgacgcg ccggtgctgc cttttttctc ctgccacatg
     4021 aagcacttca ctgattttcg caatcgtggc aacatagtaa gccagtatac actccgctag
     4081 cgctacatga ctggttcagg gctgcgcccc gaaacccgct aacaacctct cagctactgg
     4141 atatcacccc atgccatctg aatatgatga acaactggat tcgactgata cgcagcttcc
     4201 cggcgaatat gacctttttg atttaatggc gcaggttact gaagagaacc tgcatgcccc
     4261 tgtggatttt gggtcgcctg tcggccggga agcgttatag ctttttcgct tgcccgcgta
     4321 cgtggtaata ctccggtatt accttttatt tctttatttt catgtaatta cagtggattt
     4381 ttaatacccg ggtattactc gtgaaaacga aatattcctt ttttttcttt taattcatgc
     4441 agttgcgatg aaaatcgcgg ctgcgttagg tgtatgacca ttttgaggtt gaaaaataat
     4501 caaccatggc gggtgattta cgcaggttaa ggggagatcg tgacaaaaaa agcgttcctc
     4561 actgtatcgt tcatgcctgc atgaacgggt tattcttcct gactacagaa ttacatcgct
     4621 ccttcagttc atacatcact tttacatcac ttatacatca cttttacatc acttatacat
     4681 cacttttaca tcattccttc agctcatacg tcactttcat cctctgtgcc atttgtacat
     4741 cacccccttc ctgaacgtgc tgacagcggg ttttccggct gcgccggcaa cgcttcacgg
     4801 ccacgcaata aattgcgtcc ccgttcaccg ttttcggatg ggaagaacgc cggaaacagg
     4861 acttaccccg gctgaatggt gtgaatttcc gcgctatgca cttgtgcgca tactcatgca
     4921 tgccgtaaaa acagagcctg cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt
     4981 taccggtttc ccgtcagaaa cgccctgagg gcctctcagg cggtgctgat aacagatgtt
     5041 atggtaaatc agagtcacct gcactgttac tctgaaccgg agcgaaacag ccgcgaccag
     5101 aatccccgct ttttttcctg tgccagcgcg tcagccagac ggctaatttc ggcctgtagt
     5161 tgttccctct cctcatttcg caggcggttt tctgcttccc gcgccatctt gtcttcaagc
     5221 attagggtaa cagtctgctg cagagcgtcc agtttctgct gaatgacgtc tagctgagca
     5281 ttttccgcct ggctaacgac agatttggag tgtccctcct tgtgcctttt tggtgtctca
     5341 gaagtgcgca gctcgccata ggcccgaatc agttcactgg tctcgaactc ccggcgatca
     5401 ttttttcctg tgcgatagct gacaaggcct ttagccatgt cacgatataa ttgcgagcgc
     5461 gactttcctg ttaatttcag tgtctcttga actgtgtgcc atgccataaa agtgacagtg
     5521 tctcctgtgt gtaccgtatt gtaacagcag aacatattac tgttttaaca caaaaggtct
     5581 gaggctgccc gtgaggcgtg aaaaatacac aaaaaacctg ttgacggtgt ggttttgacg
     5641 ggcgtagtat ttcgaatact gtatataaac acattgttat aaatacagtt tttgctgttt
     5701 ttaaaagtca aagaggataa ttttatgagt acagagttaa atagcggtac tgtcggtggt
     5761 tttggtcaca tgggaccaaa tgacccctac aatgatggtc atagcggctc tggaagttcg
     5821 ggaggtagtt ttaacggtgg tggtaatggt ggccatgata atagtagtgg ttcatcttat
     5881 actgcatcct ttggtctcat cactggccga cacccgataa ctgtcccagg tacgaagaat
     5941 attaattctg tcgatctttc tgctgtcatt aataacatta tacatcatga aggtgcacgc
     6001 aataacatgt acctagatac tgcgaacaat gtaagagtgg gagtgacggg cactggctgg
     6061 caatgtctag caacggcagg catttcggct gagggtaaaa gaactttccg ctaagcgata
     6121 gactgtatgt aaacacagta ttgcaaggac gcggaacatg cctcatgtgg cggccaggac
     6181 ggccagccgg gatcgggata ctggtcgtta ccagagccac cg
//
