LOCUS       NZ_CP103678             3991 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Klebsiella pneumoniae strain 2946 plasmid pMB4773_2, complete
            sequence.
ACCESSION   NZ_CP103678
VERSION     NZ_CP103678.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174011
            Assembly: GCF_024918095.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3991)
  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 3991)
  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                   :: 153x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:11:57
            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)                     :: 5,377
            CDSs (total)                      :: 5,253
            Genes (coding)                    :: 5,139
            CDSs (with protein)               :: 5,139
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 49 of 114
            Pseudo Genes (incomplete)         :: 62 of 114
            Pseudo Genes (internal stop)      :: 16 of 114
            Pseudo Genes (multiple problems)  :: 13 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103678.1.
            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..3991
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="2946"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMB4773_2"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2017-12-04"
                     /collected_by="MDACC"
                     /genotype="ST307"
     gene            1..192
                     /locus_tag="M5S99_RS26830"
                     /old_locus_tag="M5S99_26830"
     CDS             1..192
                     /locus_tag="M5S99_RS26830"
                     /old_locus_tag="M5S99_26830"
                     /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_040198051.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLDKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            192..614
                     /locus_tag="M5S99_RS26835"
                     /old_locus_tag="M5S99_26835"
     CDS             192..614
                     /locus_tag="M5S99_RS26835"
                     /old_locus_tag="M5S99_26835"
                     /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_040214596.1"
                     /translation="MAIVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1418..1690
                     /locus_tag="M5S99_RS26840"
                     /old_locus_tag="M5S99_26840"
     CDS             1418..1690
                     /locus_tag="M5S99_RS26840"
                     /old_locus_tag="M5S99_26840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     gene            2271..3245
                     /locus_tag="M5S99_RS26845"
                     /old_locus_tag="M5S99_26845"
     CDS             2271..3245
                     /locus_tag="M5S99_RS26845"
                     /old_locus_tag="M5S99_26845"
                     /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_114269875.1"
                     /translation="MAFFNLLFVASLICFGGVMGSYSRGCRDSQNKFSKDKDENNKRAS
                     VYRFGIASAFICVPFISSFLHVDYSSIIFPVADGGGTKFIEQILLLISVSGISAYLGYA
                     LLDGLANKVLKEQVDGIDKKQQDLEAEQDEFKDELDRSKELIEQLEMDKKTTKFELGYF
                     KAISAVDKAESMMSIPDEALSVKKKLTEALDAVTESLSLVKREDVAKDDYDKLLVLKAY
                     ILKRLDRIDDALSITDELLMSNEDNPILIYNKACYQYILRRCQADNSDIKDMIRRALTI
                     KVTDPEFIRRQEKIRTKVIGNKDNDLEGLFTDAELEELKVAIK"
                     /name="hypothetical protein"
     gene            complement(3472..3584)
                     /locus_tag="M5S99_RS26850"
                     /old_locus_tag="M5S99_26850"
                     /pseudo=""
     CDS             complement(3472..3584)
                     /locus_tag="M5S99_RS26850"
                     /old_locus_tag="M5S99_26850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          complement(3473..3944)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 atgacaaaac aacagaaaac agcgctgaac atggctaaat tcatccagaa tcagtctctg
       61 ctcctgctgg ataagcttaa cgagcttgat ctcgatgtcg aggccgacct ttgtgagaaa
      121 ctccatgatg atgcggagca tcttttccgt acactgtcct cgagactgga tgaattacag
      181 gatggtaact gatggccata gtgtctatta gtgaagcggc acggcttgtt aaggttagtc
      241 gccccacaat ttacaagatg attaacagtg ggaagttaag ttacacctct gtggtaaagc
      301 acgggaaagc tattaaagtt attgatactt cagagctaat tagagtgttt ggttctcttg
      361 atggtgtaat cgatactgta aaatatgatg taaaaagtga cgcagaatct acaggtatta
      421 acagcgttgg tttacatgat ttacaacata gaatcgcttt acttgaagct gaaaacgatg
      481 gtcttaaagg ggctgttaag gctcgagatg agcatattga ttcccttcgt caggctatgc
      541 agcttctgga gcacaagcac gaaccttctt caccacccca ttccccgtgg tggaaattct
      601 ggaaaaaatc ctgatcccgc catgcttcca ttttgctctc cggccattcc ggggagttcc
      661 tgaaccttcc caaaaatcgt cagatccctg aacgctcctc accactaaaa atacccacac
      721 actacgcaaa attaaaattt tgcagataga cctttatttt caatcagtta tctattttaa
      781 attacgcaat tttatttttt gtaaggtgaa tccgagtcgt ggacgactct atggcgaatc
      841 gccgatgact tgcccacgat tcatatgtga atcacgccat ataatcagta cgttatgatg
      901 acttgactct agagtcgact tgccgggttg gtggcttttt gaccatggcg actctagagt
      961 caagtcacga gtcgaatcgc cggtgaatcg tgtggtgagt cgtccggcga cttgccataa
     1021 tgtgattgct ggtctcgaca aacccgattc ctgaacgtgc tgaaaaccgg ttttccggct
     1081 gcgccggcaa cgcttcacgg ccacgcaata aattgcgcac ccgttcaccg ttttcagtct
     1141 ggtttggtgc gggttttgag ttgcctggcc tgaattcagg ctgaaatccc cagacagtca
     1201 gtcaagtgca taacgattca tgcccgtaaa acgccctgga gcgattttga ggcgttttca
     1261 gggggtaaga cgtaggattt aatgggttac gccccagaat cgttctgagg ccgttttagc
     1321 ggtgcgtgta atgggacgtt atggtaaatc aacggcggat gcctgagtct gtgttagagt
     1381 cagcggattg tgataatcag tgactcaggg agatgttttg gctactgacg ctcaggtaaa
     1441 agaaattaat gcactcatca aaaaataccc ggactcatgc tccatctgtc atgaagtcta
     1501 tgatgaggat gatgtgacct acaccgtttt tgggtatgac cggaaaggta aaatacaggt
     1561 caccacggga tgctgtgccg gaatgctgac agagccggtt ctgctgggtg tctgtgggtg
     1621 ctttgacccg gaagaacgtg acgagatcat gcagaatcac cccatggcaa agcagttttt
     1681 cacagagtga ttccgtatct gttgagtctg aagcccgcct tgtgcgggct ttttcatatc
     1741 tgcgtgaaat gaggcgttat ggtaaatgca cgcattcatt cttttgaaaa atccagaatg
     1801 acgaatacat ggggcatgtt tatatgacta ttgagaggaa ggatgttatt gtaaaaaaat
     1861 cctttaaatt caatcattta attatggtag ccaaaggggc ggggcttcgc ttattcctaa
     1921 ggaataagcg aagccccgcc cctttggcta ccagtgcatt atactttttt tttcacccaa
     1981 tgtcaataca tgggttgatt ttatcatttt aagcattttt gttgttgtga gtgctgggtt
     2041 tatgccctat attcagcgct aagcaagcat gggcttgcaa aggaacaatt aatgagaggt
     2101 gctctatgaa aaaaatcaaa cttcacgatg agcgtccaga cttgtaagtg tcaagtcagc
     2161 agaaaaaggc agccaaggct gccttttttg ttattggtta gtatatgatt gagcttatct
     2221 taacttacct gaacaaagtt ttattgtttg ctttgcgcaa ggattctctc atggcttttt
     2281 ttaacctatt gtttgttgca tctctaattt gttttggtgg tgttatgggg agctattcca
     2341 gaggttgccg agactcccaa aataaatttt caaaagataa ggatgagaat aataaaagag
     2401 ctagtgttta tagatttggt atagcatccg catttatttg tgttcctttc atatcatcat
     2461 ttcttcatgt tgattactca agtataatat ttcctgtggc tgatggtggt ggaactaagt
     2521 tcatagaaca aatattgctt cttatttctg tttcggggat ctctgcgtat cttgggtacg
     2581 cattactgga tggtcttgcc aacaaagtat taaaagagca agtagacggt atagataaaa
     2641 agcaacaaga tttggaggct gaacaagatg agtttaaaga tgagcttgat aggagcaagg
     2701 agctgataga acagcttgaa atggataaga aaacaacaaa attcgagcta ggatacttta
     2761 aagccatttc agctgtggat aaagcagaat caatgatgtc cattccggat gaggctcttt
     2821 ctgttaagaa aaaactaact gaggcattag atgctgtaac ggaatcattg tctcttgtta
     2881 aaagagagga tgtagctaag gatgactacg acaagctctt agtgcttaaa gcttatattt
     2941 tgaaaagact tgatcgtatt gatgatgctc tgtcaattac ggatgagtta cttatgagta
     3001 atgaggataa ccctatactt atttacaata aggcttgcta tcaatatatt ttgcgtcgtt
     3061 gccaagctga taactccgat attaaggata tgattcgcag ggctctgact attaaagtta
     3121 cagatcctga attcattcgc aggcaagaaa aaataagaac caaggtcata ggaaataaag
     3181 ataatgatct tgaagggttg tttactgacg ctgagctgga ggaattaaag gtggctatca
     3241 aataggcagt ggctagctct atgaattcca aaaagatcct tgacgatcct ttgaggtgca
     3301 gcgtactcta cccctcaaac gaaaaaacca cccggcaagg tggtttttcg aaggttcagt
     3361 aaccggcaag tttctgaacc gaggtaactg gcttagagga gcgcagtcac caaaacagtt
     3421 cgtttagttt agccttaact ggcgcataac ttcaagacta actcctctaa atcaattacc
     3481 agtggctgct gccaatggcg ataagtcgtg tctttccggg ttggactcaa gagatagtta
     3541 ctggaacggg cgcagcagtc ggactgaacg gggggttcgt gcatacagtc cagcttggag
     3601 cgaactgcct tcccggagcc gagtatcagg catggaatga gaaaacgcgg ccataacagc
     3661 ggaatgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccaccaggg
     3721 ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca ccactgattt gagcgtccgt
     3781 ttccgcgatg cttgtcaggg gggcggagcc tatggaaaaa cagccgttcg gcggcctttg
     3841 cttttctgcc tcatatcttg gttgcctacg tttttatgta cacgctcctg ccgctcgccg
     3901 cagccgaacg gctggagcgt agcgactgag tgagcgagga agcggaaaag agactagttt
     3961 gacattgagc actgacgctc tgaggcttct t
//
