LOCUS       NZ_CP054167             4063 bp    DNA     circular CON 10-DEC-2023
DEFINITION  Escherichia coli strain STO_Bone1B plasmid pBone1B_2, complete
            sequence.
ACCESSION   NZ_CP054167
VERSION     NZ_CP054167.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15006794
            Assembly: GCF_021498165.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4063)
  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  JOURNAL   Unpublished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 4063)
  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                   :: 1210x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/10/2023 02:32:15
            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)                     :: 4,863
            CDSs (total)                      :: 4,743
            Genes (coding)                    :: 4,472
            CDSs (with protein)               :: 4,472
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 271
            CDSs (without protein)            :: 271
            Pseudo Genes (ambiguous residues) :: 0 of 271
            Pseudo Genes (frameshifted)       :: 101 of 271
            Pseudo Genes (incomplete)         :: 154 of 271
            Pseudo Genes (internal stop)      :: 74 of 271
            Pseudo Genes (multiple problems)  :: 53 of 271
            Pseudo Genes (short protein)      :: 4 of 271
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054167.1.
            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..4063
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STO_Bone1B"
                     /isolation_source="bone infection of foot"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBone1B_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(3673..4063,1..1757)
                     /gene="mobQ"
                     /locus_tag="HRS04_RS00955"
                     /old_locus_tag="HRS04_00940"
     CDS             join(3673..4063,1..1757)
                     /gene="mobQ"
                     /locus_tag="HRS04_RS00955"
                     /old_locus_tag="HRS04_00940"
                     /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_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2005..2706)
                     /locus_tag="HRS04_RS00960"
                     /old_locus_tag="HRS04_00945"
     CDS             complement(2005..2706)
                     /locus_tag="HRS04_RS00960"
                     /old_locus_tag="HRS04_00945"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3240..3494)
                     /gene="mobC"
                     /locus_tag="HRS04_RS00965"
                     /old_locus_tag="HRS04_00950"
     CDS             complement(3240..3494)
                     /gene="mobC"
                     /locus_tag="HRS04_RS00965"
                     /old_locus_tag="HRS04_00950"
                     /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_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3496..3672)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3673..4031
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2006..2706)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..1754
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.578"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atccccatgc gcacatcatg ctgaccacga gggctatcgg acctgctggg ttcagcggaa
       61 aggtcaggga ctggaacgac cggacacatg ccgagacgtg gcgggcatca tgggctgacc
      121 atgcaaacag ggcactggcg aacgccggtt atcaggaaga gatagaccat cgttcatacg
      181 agcgacaggg gcttgagaaa acgcctggta ttcacctcgg aaagtctgcc tgtgcgatgg
      241 aaacacgcgg tatcgaaaca gaacgcggcg aacagaatcg tctgattaac aggcttaacc
      301 tggaaataca gatttcccgc accgaactca ggaacggagg gctgacagag cctgcccgcc
      361 gtgtggctga ccttctgaat atcgggcttc ctgacaacgc aacttcgtac acactacgtg
      421 acattatcga agcgttgccg aaggacagta actcggcatg gaaactcacc agtaatgcca
      481 tgtcgatgat ggcagatatg caggcgacgc gcagacgctg ggaagagctg aacaccgaac
      541 gaaaggaagc gatgagccat gctgccagcc tgaaaaaatc atcgccgttt tcgtccggtt
      601 tttcccgtat tcccctgatg caatgggcgg caccggaata ccgtagtgag cagggaaaaa
      661 tccagtctct gagccagcaa atggaaaaat tacgacagca ttaccggaag gtggagaaac
      721 aggacattcc cgcgagtcag atggcatttg aaaaacagtg gcagcagtgg ggggaatccg
      781 gccttgcagc tctcagagcc cagttgctta aacgtgaaga ggaattgcgc cggaaggaac
      841 aggaagatac tgaacgtagt cgcgcggagc agctcaggaa aaatgacaat gccgttatgg
      901 attcaggggt gctgagagca gtcgttacgg ggtatggcga ggctcccatg cctggtaacg
      961 gggaaatgac ctgttacctt ctgcttcaca accggaacgg agaatatacg ctctggggga
     1021 acgagctgga gaaataccgc accagaatct ttgagagtgt tgatttaatg cgtgacagga
     1081 gtggttatat ctgtgaccga agcgaaatcg gccaacgtcc gccactgcaa cgtgtttatt
     1141 cctctgcaac ctttgagcaa ctgctgacgc aggtttgcca gacatggccg caacataccc
     1201 gcaatctccg ccagccgaag acatggccgg agtctttctg tcttggagaa gaccgccagc
     1261 cagccatgcc atcaccagcg gcaaggaagg tggattttat gcagggacgt ctgccaccga
     1321 cgctgatgcc ggtcatgagt tctgtcgacc gggaaacccg ccagcttcag cttttgctgg
     1381 tcatgggcgt ggatgactct ctgggcggtg ttatccggct taatggtacg ctgtatcccg
     1441 cgtttgccgt tccctcagcc gataacaggc atctggtcat cagtgcgctg accgataagg
     1501 ggttacggta tgcagggtat ggtgttgccg taaatcacga tgcagacagc cacatatcac
     1561 ctgcaccaga actgatgcag tttcatctga aaacccgtga ggcaccgctt tttgctgccg
     1621 tcaacacacc agaaaaacag ccggatcatc tgttccgctc gctgggtttt aatcgtacct
     1681 gggaggaatg gcagcgcgag gaagatgcac gaacacacac caccgagagg agacatgatc
     1741 gcggttggtc acagtgaatg tgaacaatat tttgttttgt ttaacatcgt gttatgttcg
     1801 tcgatgttca tcgacaggga tgaatgcaag aagcacactc acataacgca agcatagttt
     1861 tgtttttccg cccccaaaaa ttggggggtc ttttttcgct gcatcagagc gtttttgacg
     1921 caatttttca cttcaatagt accttcgcac tactaacaca aaaaaaacgc agcagggagc
     1981 gttttaggtg ccttaaaatc gattttagat cgtcatcttg atctgtttgt cttccttgaa
     2041 gcgaaaatgc agggctacaa ccgtgcgccc ctttttgatc gtctcaacag ttacaaccag
     2101 atcgcttttt tcgttcagtt cggcgatggc tggcttgatt atcatcttat tcaagtcttt
     2161 gaattgttga tatttatctt caacggcaag catggttcgg aaatcatcga tagctatcgt
     2221 tctgtcaccg gtgctgcgga actgctggag cagctcgtaa atgcggatgc tgtaggtgct
     2281 ggaaaggctg gagacgttct tcacgactac ccgcgtaaac tgccccttga gctgtgtcag
     2341 atacggcatg atggcatcgg agaaggtgat atctactttc gcctcacctt tgaaatactg
     2401 cgcccggtac tgcacccagc ggaactcttc tcgtttttcc tcgttcttga tgattactga
     2461 cctgtcccag aggcgatcta tcgcttcctt gagcctagct tcagcgtgct gccgtcccat
     2521 gtcaggaaag gcatcatgaa actctgcagc cgtgatggtc atggtttttt gttcatccgg
     2581 cgaaggggaa tcttctccgg attttaggcg gctgatacag accagcagga agcgctgttc
     2641 ctgcaaagtg agcttgtagc ttgcctcgat aagggcgttt gatttgtaag ctatcagatc
     2701 tgacatttcg cttgctcgtt gctattggtg gcgttttttt actgtacgcc acttatcata
     2761 tgggtggaag tttttttttt gcaaccccct ttttctgtgg attacacccc caaaagctcc
     2821 acctttcacc cccaaaagct ccacctttca cccccaaaag ctccaccttt cacccccaaa
     2881 agctccactt atcttgccag aacatcttta aaatcatggt gttacaagac ctaaaaaggt
     2941 tttaaaaaaa aagatctaaa aataagatct taaaaactta acggcgagcc tgtggataac
     3001 ttggggtgct gaaaacaaaa aaccaataaa aacaatgcgt tgcaataaag cagaattgca
     3061 agtttcgaat acaccccctc caaccctgtg gaaacccagt attcatgcgg gttcagcgca
     3121 tatcacctgc cgaaaaaccg tgcgtatgtg ctcaacctgg cgactgattc acttccgctt
     3181 cctcgcccac tcgctcgcta acgctcggtc gctggggctg cggcgagcgg acgatacaat
     3241 cactgttctg gcagcgcctc cagctcgtta atcagcggca gtatgcgcgt cacatcagcc
     3301 tgtcgtgtca cctctgcctt caggaactgg agtaaccagg cacgcaactg cacctcctcc
     3361 ggctttctga cctttgccag caatgcagca cccacaacaa ccttctgcgc tgtgtccagg
     3421 ctccggctct tcgccttcag gcgctgtaat ctcgcctcag catcagcaat cttctgttcg
     3481 agcgttctgc tcatgatgta actccgtgcg cgatgaaaaa tcgcatttta gcgcgtcact
     3541 ggtagtttaa aaactgagct ggcataatgc acggcaaatc acgaagtgcg cacttataca
     3601 atctccactc cgtttcgatt gtgtgcgccc tgcggggctg aaagaaaact acaaaaaggc
     3661 attacggcag aaatggcgat ttatcatctc agcatgaaaa ttatctccag aagcagcggc
     3721 tacagcgccg tagcttccgc tgcctatcgt tccggttcac tgatgcttga tgagcgtacc
     3781 ggactgactc acgactacac ccgcaaaagc ggtgtggctg aggctgtgat tctgaccccc
     3841 gccaccgccc ctgcctggtg tacgaaccgt gccgaactct ggaatgccgt tgagaaggcc
     3901 gaacgccgga agaactcaca acttgcgcgg gaaattgaac tcgccatccc ccacgaactg
     3961 ccgcaggatg ccgcacggga aaccgttctc gcctttgtca gagaaaactt tgtcagtcag
     4021 ggcatgattg ctgatgtggc gttccatcac atggataaaa caa
//
