LOCUS       NZ_CP103569             4773 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Klebsiella pneumoniae strain 4680 plasmid pMB8190_2, complete
            sequence.
ACCESSION   NZ_CP103569
VERSION     NZ_CP103569.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174066
            Assembly: GCF_024917255.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4773)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 4773)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 168x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 05:36:13
            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)                     :: 5,322
            CDSs (total)                      :: 5,200
            Genes (coding)                    :: 5,037
            CDSs (with protein)               :: 5,037
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 51 of 163
            Pseudo Genes (incomplete)         :: 114 of 163
            Pseudo Genes (internal stop)      :: 18 of 163
            Pseudo Genes (multiple problems)  :: 18 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103569.1.
            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..4773
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="4680"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMB8190_2"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-05-04"
                     /collected_by="MDACC"
                     /genotype="ST29"
     gene            1..192
                     /locus_tag="M5S58_RS26545"
                     /old_locus_tag="M5S58_26545"
     CDS             1..192
                     /locus_tag="M5S58_RS26545"
                     /old_locus_tag="M5S58_26545"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            192..614
                     /locus_tag="M5S58_RS26550"
                     /old_locus_tag="M5S58_26550"
     CDS             192..614
                     /locus_tag="M5S58_RS26550"
                     /old_locus_tag="M5S58_26550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_048290308.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKHTKVID
                     TSELIRVFGSLYGGDDTVKHDVKGDAGATAVNILGLHDLQHKIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSPQVHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1423..1836
                     /locus_tag="M5S58_RS26555"
                     /old_locus_tag="M5S58_26555"
     CDS             1423..1836
                     /locus_tag="M5S58_RS26555"
                     /old_locus_tag="M5S58_26555"
                     /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_071997596.1"
                     /translation="MTIPKIKSFPEVGSRREEQAHFVWIALTSWCLFNKNKTITYGELA
                     KLIGYPAQAGRTLAEALGTVSLYCLYNDLPPLSCIVVAKNTNHPGWEGMIPSNSSLEKE
                     QNKVWETSWNLYRTPSVGTLRRAREELNWDEFI"
                     /name="hypothetical protein"
     gene            1954..2244
                     /locus_tag="M5S58_RS26560"
                     /old_locus_tag="M5S58_26560"
     CDS             1954..2244
                     /locus_tag="M5S58_RS26560"
                     /old_locus_tag="M5S58_26560"
                     /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_226554717.1"
                     /translation="MVRLIKDDRLRTLATFDGKTLKDDRLRTLATFDGKTLKDDRLRTL
                     ATFDGKTLKDDRLRTLATFDGKTLKDDRLRTLATVDGSVSIVIIAFAARIF"
                     /name="hypothetical protein"
     gene            complement(2779..3669)
                     /locus_tag="M5S58_RS26565"
                     /old_locus_tag="M5S58_26565"
     CDS             complement(2779..3669)
                     /locus_tag="M5S58_RS26565"
                     /old_locus_tag="M5S58_26565"
                     /inference="COORDINATES: protein motif:HMM:NF015983.3"
                     /GO_function="GO:0051539 - 4 iron, 4 sulfur cluster binding
                     [Evidence IEA]; GO:0003824 - catalytic activity [Evidence
                     IEA]; GO:1904047 - S-adenosyl-L-methionine binding
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="radical SAM protein"
                     /protein_id="WP_048290309.1"
                     /translation="MFELKSPLLLVIDITNECNLSCNYCFQDFRSDTKNSINLGTITEI
                     LSEAKDMGIFEINICGGEPFKHKDIINIISEVKRVGFNLSIVTNGTLINKKTALLLNEL
                     DVIKNMQISFDSHIDSIHNKLRGGYHQAIRGLDYLLSYDSPPPSIGIVISKENVNHINE
                     TIDFFSRKGIRRFHIMNLLGNKELSCSDAELNEATKRINESFLQSRDGDKKLIISNLDF
                     KEKKDYQYKDVHINCLAGYTTLVLTSSLNIIPCDMVNYIIKKWKKKGDLRDGFELSKKQ
                     WLGLKESWCKGCFKC"
                     /name="radical SAM protein"
     gene            3806..4030
                     /locus_tag="M5S58_RS26570"
                     /old_locus_tag="M5S58_26570"
     CDS             3806..4030
                     /locus_tag="M5S58_RS26570"
                     /old_locus_tag="M5S58_26570"
                     /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_197986819.1"
                     /translation="MKIKLLDSVYNVEPKTDIMAWDNHWNYQWSGRTSGITKDAIKWRK
                     ESDGQFIVCDETGAVWLVDQNELDNLLAA"
                     /name="hypothetical protein"
     gene            complement(4245..4358)
                     /locus_tag="M5S58_RS26575"
                     /old_locus_tag="M5S58_26575"
     CDS             complement(4245..4358)
                     /locus_tag="M5S58_RS26575"
                     /old_locus_tag="M5S58_26575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071997595.1"
                     /translation="MHEPPVQSDCCACFGNYRLESNPKRHDKTPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(4246..4653)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.484"
                     /coverage="99.0"
                     /evalue="1.3e-157"
ORIGIN
        1 atgacgaaac aacagaaaac agcgctgaac atggctaaat tcatccagaa tcagtctctg
       61 ctcctgctgg agaagcttaa cgagcttgat cttgatgctg aggccgacct ttgtgagaaa
      121 ctccacgatg atgcggagca tcttttccgt acactgtcct cgagactgga tgaattacag
      181 gatggtaatt gatggccaga gtgtctatta gtgaagcggc acggcttgtt aaggttagtc
      241 gccccacaat ttacaagatg attaacagtg ggaaactaag ttacacctct gttgtaaagc
      301 atgggaaaca tactaaagtt attgatacat cagagcttat tagggttttt ggctcgctgt
      361 atggtgggga cgacactgta aaacatgatg taaaaggtga cgcaggcgct acagcggtta
      421 acatccttgg tttacatgat ttacagcata aaattgcttt gcttgaagct gaaaacgatg
      481 gtcttaaagg ggctgttaaa gctcgtgatg aacatatcga ttctcttcgc caggctatgc
      541 agcttctgga gcacaagcac gaaccctctc cacaggttca ttctccgtgg tggaaattct
      601 ggaaaaaatc ctgatcctgc catgcttgag ttttcctctc cggccatccc ggggagttcc
      661 tgaaccttcc caaaaatcgt cagatctctg aacgctcctc accactaaaa atacccacac
      721 actacgcaaa attaaaattt tgcagatata cctttatttt caatcagtta tctattttaa
      781 attacgcaat tttatttttt gtaaggtgaa tccgagtcgt ggacgactct atggcgaatc
      841 gccgatgact tgcccacgat tcatatgtga atcacgccat ataatcagta cgttatgatg
      901 acttgactct agagtcgact tgccgggttg gtggcttttt gaccatggtg actctagagt
      961 caagtcacga gtcgaatcgc cggtgaatcg tgtggtgagt cgtccggcga cttgccataa
     1021 cgtgattgcc ggccgtcgac gaacccgatt cctgaacgtg ctgaaaaccg gttttccggc
     1081 tgcgccggca acgcttcacg gtcacgcaat aaattgcgtc cccgctcacc gtttgcagtc
     1141 tggtttggtg cgggttttga gttgtctggc gtgaattcag gctgaaatcc gccaccaatc
     1201 agtctggtgc ataacaattc atgcccgtaa aaagccctgg ggcgattttg aggcgttttc
     1261 agggggtaag atgtaggatt tgatgggtta cggcccagaa tcgtttctgg ggcgtttgag
     1321 cggtgcgcgt aatgacgcgt tatggtaaat agttttttgt acgcactcat cttttggtat
     1381 attataaagt gaaaatatga acggtttgtg agaattttaa caatgacaat tccaaaaata
     1441 aaatcatttc cagaagttgg ttcaagaaga gaagagcagg ctcattttgt gtggatcgct
     1501 ttgacgtcat ggtgtttgtt caataagaat aaaacaatca catatggaga acttgcgaaa
     1561 cttattgggt atcctgcgca agcaggacgc actttagctg aggctttagg tacagtctca
     1621 ctgtattgtt tatataacga tcttcccccc ttaagttgca ttgttgttgc caaaaatacc
     1681 aatcatcccg gatgggaagg aatgatccct tcaaattcat cattagaaaa agaacaaaat
     1741 aaggtatggg aaacatcgtg gaatctatat aggacaccat cggttggaac gttaagaaga
     1801 gcgagagagg aacttaattg ggatgaattt atttaatttt atgaaaagta atattcagaa
     1861 ttaatccaaa cctgagaaaa atgaatttct aataggggat gtatatgact ataactataa
     1921 aagatgacag gttaagaact ttagcgacct ttgatggtaa gactcatcaa ggatgacaga
     1981 ctaagaacct tggcgacctt tgatggtaaa actctcaagg atgacaggtt aagaactttg
     2041 gcgacctttg atggcaagac tctcaaggat gacaggttaa gaactttggc gacctttgat
     2101 ggtaagaccc tcaaggatga caggctaaga actttggcga cctttgatgg caagaccctc
     2161 aaggatgaca ggctaagaac cttagcaact gtagatggtt cggtaagtat tgtaattatc
     2221 gcttttgccg cccgcatctt ttgacttttt ttataaaaaa gtacttatat ctacaggtgt
     2281 tataaatgag tatgattttt ttgtaaaaaa aacaacgccc cagaaatcgt ggactcaact
     2341 tggcggtaga ttcccaatta ctagggcgca ggtacaaaac ctaaaaggat attagcgcat
     2401 gaaatgcgcc aaacaacagc ccgccataag ctcatgctac attgactagc catgccattg
     2461 atctattcag tctgcgtttg ccaaagaaac cgtaccacgg gtatgaagtc caatggaacg
     2521 gaaacgtacg ttagttaagt aagtgtctga tatatcgaaa cataatggac attgaaaaac
     2581 gccctcaaaa cggtgtcttt ttaatcgaaa attggcattt aacggacagg cttgtctata
     2641 aatcgatttt tcagacgata attttcctct taccgtacgt tttcgtacgg ttggccatca
     2701 aaccccatta aaaagatttt tagtattcag tatagagtag tggaaaacta ttttactcgc
     2761 atttacatgt taatacactt agcatttaaa acaaccctta caccatgatt cctttaatcc
     2821 aagccattgt ttttttgaaa gttcaaagcc atcacgcaaa tcaccttttt ttttccattt
     2881 ttttataata taattaacca tatcgcaagg tattatattt aaagatgatg tcaagactaa
     2941 cgtagtgtat ccggcaaggc agttgatgtg cacatcttta tattgatagt ctttcttttc
     3001 tttaaaatct aagttggata ttattaattt tttatcgcca tctcttgatt gtaaaaatga
     3061 ttcatttatt ctttttgttg cttcgtttaa ttcagcatct gaacatgata gctctttgtt
     3121 acccagtagg ttcattatgt gaaatctgcg tattcccttc ctggaaaaaa aatctatagt
     3181 ttcatttata tgattaacat tttctttact tataactatg cctattgatg ggggagggga
     3241 atcataagaa agcaagtagt ctaaccctct aattgcttga tggtaacctc ctcttaactt
     3301 gttgtgaatg gaatctatat ggctatcaaa actaatctgc atgtttttta taacgtcaag
     3361 ttcattgagt agtaatgctg tttttttatt gatcaatgta ccgttagtta caatggataa
     3421 attaaaccca actctcttta cttcagatat tatatttata atatctttgt gcttaaatgg
     3481 ttctccgcca catatgttta tctcaaaaat acccatatct tttgcttctg ataatatttc
     3541 ggtgattgta cctaagttga tgctgttttt agtatccgat ctgaaatctt ggaagcaata
     3601 attgcatgat aaattacact cattggttat atcaatgacc aatagcaatg gtgatttcaa
     3661 ttcgaacata atcgttaccc tgtgtttttg gtttttatta tatttttcaa ttaattgatt
     3721 agtcttgacg gtagtcaata aaattcgatt cagtatttta tatgctcatc tgtagttcta
     3781 gattttttct tgagaggtaa ttgcggtgaa aatcaagctg ttagattcgg tttataacgt
     3841 agagcctaaa acggatatca tggcgtggga taatcattgg aattatcaat ggagtggccg
     3901 tacatcggga attacgaagg atgccattaa gtggaggaaa gagtctgatg ggcagtttat
     3961 tgtttgtgat gagacaggag ctgtctggct agtagatcag aatgagttgg ataacttgct
     4021 cgctgcataa cgccatattt ctagtattta cttgagatcc tcaccttccc atcgtaatct
     4081 tctcccctga aagagaaaaa ccgcccagca aggcggtttt tcaaaggttc tctgagcagc
     4141 aactctttga accgaggtaa ctggcttgga ggagcgcagt aaccaaaact gttcgtttag
     4201 tttagcctta actggcgtat gacttcaaga ctaactcctc taaatcagtt accagtggct
     4261 gctgccagtg gcgttttgtc gtgtcttttc gggttggact caagtcgata gttaccgaaa
     4321 caggcgcagc agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact
     4381 gcctacccgg aactgagtgt caggcgtgga atgagataaa cgcggccata acagcggagt
     4441 gacaccggta aaccgaaagg caggaacagg agagcgcacg agggagccgc ctatcagaaa
     4501 tgataggtat ctttatagtc ctgtcgggtt tcgccaccac tgatttgagt gtcagatttc
     4561 gtgatgcttg tcaggggggc ggagcctatg gaaaaacggc cgcttagcgg cctttccttt
     4621 tccccgtcac gcgaccgctc ggttttctcg agcttttaca cgcatgctcc tgccgctcgc
     4681 cgcagccgaa cggcaggagc atagcgactg agtgagcgag gaagcggaaa agagaacatc
     4741 cctacactga gcactgacgc tgtgaggcct ctt
//
