LOCUS       NZ_CP073046             5309 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. MGH103 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP073046
VERSION     NZ_CP073046.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03280163
            Assembly: GCF_001034475.2
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. MGH103
  ORGANISM  Citrobacter sp. MGH103
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5309)
  AUTHORS   Earl,A.M., Manson,A.L., Bhattacharyya,R., Brennan-Krohn,T.,
            Cosimi,L., Delaney,M., Ferraro,M.J., Gilmore,M., Gussin,G.,
            Hooper,D., Huang,S., Kim,D., Kirby,J., Onderdonk,A., Peterson,E.,
            Pierce,V., Shenoy,E., Wurster,J., Shea,T.D., Chapman,S., Howe,W.,
            Walker,B. and Birren,B.W.
  TITLE     Multi-genus dynamics of carbapenem resistance within hospitals
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5309)
  AUTHORS   Earl,A.M., Manson,A.L., Bhattacharyya,R., Brennan-Krohn,T.,
            Cosimi,L., Delaney,M., Ferraro,M.J., Gilmore,M., Gussin,G.,
            Hooper,D., Huang,S., Kim,D., Kirby,J., Onderdonk,A., Peterson,E.,
            Pierce,V., Shenoy,E., Wurster,J., Shea,T.D., Chapman,S., Howe,W.,
            Walker,B. and Birren,B.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-MAY-2021) Infectious Disease and Microbiome Program,
            Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 5309)
  AUTHORS   Earl,A.M., Manson,A.L., Bhattacharyya,R., Brennan-Krohn,T.,
            Cosimi,L., Delaney,M., Ferraro,M.J., Gilmore,M., Gussin,G.,
            Hooper,D., Huang,S., Kim,D., Kirby,J., Onderdonk,A., Peterson,E.,
            Pierce,V., Shenoy,E., Wurster,J., Shea,T.D., Chapman,S., Howe,W.,
            Walker,B. and Birren,B.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-AUG-2020) Infectious Disease and Microbiome Program,
            Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
REFERENCE   4  (bases 1 to 5309)
  AUTHORS   Earl,A.M., Onderdonk,A.B., Kirby,J., Ferraro,M.J., Huang,S.,
            Spencer,M., Fodor,A., Hooper,D., Dekker,J., O'Brien,T., Quan,V.,
            Gombosev,A., Delaney,M., DuBois,A., Ernst,C., Kim,D.S., Rossman,W.,
            Gohs,F., Petruso,H., Nozar,T., Mougeot,F., Manson-McGuire,A.,
            Young,S., Abouelleil,A., Cao,P., Chapman,S.B., Griggs,A., Priest,M.,
            Shea,T., Wortman,I., Wortman,J.R., Nusbaum,C. and Birren,B.
  CONSRTM   The Broad Institute Genomics Platform, The Broad Institute Genome
            Sequencing Center for Infectious Disease
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2015) Broad Institute of MIT and Harvard, 7
            Cambridge Center, Cambridge, MA 02142, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.3
            Assembly Name                     :: MGH103
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 207x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:23:32
            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)                     :: 5,298
            CDSs (total)                      :: 5,175
            Genes (coding)                    :: 5,057
            CDSs (with protein)               :: 5,057
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 32 of 118
            Pseudo Genes (incomplete)         :: 85 of 118
            Pseudo Genes (internal stop)      :: 19 of 118
            Pseudo Genes (multiple problems)  :: 18 of 118
            Pseudo Genes (short protein)      :: 1 of 118
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073046.2.
            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..5309
                     /organism="Citrobacter sp. MGH103"
                     /mol_type="genomic DNA"
                     /strain="MGH103"
                     /host="Homo sapiens"
                     /db_xref="taxon:1686378"
                     /plasmid="unnamed3"
                     /collection_date="2014"
     gene            59..268
                     /locus_tag="SK33_RS26295"
     CDS             59..268
                     /locus_tag="SK33_RS26295"
                     /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_032201350.1"
                     /translation="MTKFEAFKDQITNAAKASFPEWVTFEYENDFPGYNESFVYESVCA
                     IKKMGELEVRNNADRYFSVKFISA"
                     /name="hypothetical protein"
     gene            complement(324..704)
                     /locus_tag="SK33_RS26300"
     CDS             complement(324..704)
                     /locus_tag="SK33_RS26300"
                     /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_032201349.1"
                     /translation="MKKITSLLLLGVFGLTGCAQNVSPQVAAQAQAPIYCENKQQCDAY
                     WTKAKAWIAMNSGWKIQMADETVIATYSPIGNSAILGYQVVKTPIGGERHEIVVQTACA
                     NMFGCIPNAIEQTAKLKNYIKN"
                     /name="hypothetical protein"
     gene            1999..2199
                     /locus_tag="SK33_RS26305"
     CDS             1999..2199
                     /locus_tag="SK33_RS26305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045351243.1"
                     /translation="MSLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(2247..2436)
                     /locus_tag="SK33_RS26310"
                     /pseudo=""
     CDS             complement(2247..2436)
                     /locus_tag="SK33_RS26310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2715..2924
                     /locus_tag="SK33_RS26315"
     CDS             2715..2924
                     /locus_tag="SK33_RS26315"
                     /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_215263282.1"
                     /translation="MTKFEAFKDQITNAAKASFPEWVTFEYENDFHGYNESFVYESVCA
                     IKKMGELEVRNNADRYFSVKFISA"
                     /name="hypothetical protein"
     gene            complement(2980..3360)
                     /locus_tag="SK33_RS26320"
     CDS             complement(2980..3360)
                     /locus_tag="SK33_RS26320"
                     /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_032201349.1"
                     /translation="MKKITSLLLLGVFGLTGCAQNVSPQVAAQAQAPIYCENKQQCDAY
                     WTKAKAWIAMNSGWKIQMADETVIATYSPIGNSAILGYQVVKTPIGGERHEIVVQTACA
                     NMFGCIPNAIEQTAKLKNYIKN"
                     /name="hypothetical protein"
     gene            4655..4855
                     /locus_tag="SK33_RS26325"
     CDS             4655..4855
                     /locus_tag="SK33_RS26325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045351243.1"
                     /translation="MSLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(4903..5091)
                     /locus_tag="SK33_RS26330"
     CDS             complement(4903..5091)
                     /locus_tag="SK33_RS26330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1011..1501)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.122"
                     /coverage="81.0"
                     /evalue="0.0"
     Typing          complement(3665..4156)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.929"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 taattctttc tgtggtaaaa tctctctgag ccacccggtt cttacatagg atatatccat
       61 gaccaagttt gaagctttca aagatcagat aacgaatgcc gctaaagcat cttttcctga
      121 gtgggtaacg tttgaatatg aaaatgattt tcctggatat aatgaatcct ttgtttatga
      181 atccgtctgt gctattaaaa aaatgggtga gttagaagta agaaataatg cggacagata
      241 ttttagtgtg aagtttatat cggcctagca tgtttgattg tttcggaaag cccgataaac
      301 gtgggctttc atgaatataa tcatcagttt tttatgtagt tttttaattt tgctgtttgt
      361 tcgatggcat taggaatgca gccaaacata ttggcgcagg ctgtttgaac gacaatttcg
      421 tgcctttccc ctccaattgg agtttttacc acttgatatc ctaaaattgc actattacca
      481 ataggtgagt acgttgcaat aaccgtttca tccgccattt gtattttcca gcctgaattc
      541 attgctatcc aagcttttgc tttagtccag taagcatcac attgctgctt attttcgcaa
      601 tatataggcg cttgagcttg agctgctact tgtgggctga cattttgagc gcagccggtc
      661 aagccaaaga ctccgagtaa taatagagaa gttatttttt tcattttaag cctctgttgt
      721 ttattgtttt ttatgtgctg attttaacat tatctatacg taggaaagaa gaaagtaggt
      781 gtggttaggt tgcaaaagaa aaatgatctt cttgagatcc ttttgagcag cgcgtaatct
      841 cctgctctgt aaacgaaaaa accgccttgc agggcggttt ttcgaaggtt ctctgagaga
      901 tcaactcttt gaaccgaggt aactggcttg gaggagcgca gtcaccaaat ctgtccttcc
      961 agtttagcct taaccggccc ataacttcaa gactaactcc tctaaacagt tatcagtggc
     1021 tgctgccagt ggcgcgttgt cgtgtctttc cgggttggac tcaagtcgat agttaccgga
     1081 caaggcgcag cggtcggact gaacgggggg ttcgtgcata cagtccagct tggagcgaac
     1141 tgcctacccg gaactgagtg tcaggcgtgg aatgagataa acgcggccat aacagcggaa
     1201 tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcca ccagggggaa
     1261 acgcctggta tctttaagtc ctgtcgggtt tcgccaccac tgatttgagc gtcagatttc
     1321 gtgatgcttg tcaggggggg cggagcctat ggaaaaacgg cttcgccgtg gccttcttgc
     1381 ttccctgtta agcttcttcc tggaagatgc caggaaattt ccgccccgcc agtaagccgg
     1441 taccgctcgc cgcagccgaa cgaccgagcg gagcgagtca gtgagcgagg aagcggaata
     1501 tctccaggct tatctttggc accgtacgcg ccatagctgc atttttttat acgatgcagg
     1561 atagggctaa cgccgcaaaa tgacgtcatc cgacatcatt ccgccgcgtt cgcccagtga
     1621 cctacagtcg gctctggggt gtcggggctg tgccctgacc gggcgttttg gagtatcgcc
     1681 accgtggtgg cggtgctaca aaacatatcc tgtcccttcc ttggcatctc tgaagtttag
     1741 cctgtataca ctccgctagc gctacgtgac tggttcaggg ctgcgccccg acacccgcta
     1801 aaagcactga cgcgcctgcg gtttgcccaa ccccgcgccg tccgggaaag aatttcccga
     1861 tcgacccgac gtttctgttt acctgtgatg ttaacgtttg gatctttttc ccgggtttac
     1921 ctattttctt ctaatgaagc gttcacagct gacgttaata gatgggtgct tcatgtttgg
     1981 tttttcaccg gagaacttat gagcctttgc cccgatgaac gtctgctctt tgtgcggatg
     2041 atttccgcta tgcttcgccg ttcgggcggt gatgcgggtg ctgttatgtt tgaggcgtat
     2101 cgccatattg tgtccgatac caatcaagct cgtcgttcct acatgctcga cctgctcgaa
     2161 agcgtcaggc atgactatgt acacggtgga tatacatagt tgccccggat acgcttttcg
     2221 tctaagtgag cgttcttttc gtctctttat tcgccgtcct gtataccgaa gcgtgcgctc
     2281 agcttctgat aaagcgcttc tgcctgttcg tgcattcgct cacagtcggc tgcctcgtca
     2341 tcaagatcga gcacgtcgag ttttttcgag cagcagcagc gactgcgccc ggataaattt
     2401 tgccatgttc agtgcggctg attcctgttt tgtcatacgg ctttttttcc cggttttatg
     2461 gtgatcgcag actgaaatct tacttcattc acttgagtgc atagccatgc aggtacgcag
     2521 aaatcatcag cgcgtttctg agcggttttc agggggtaag atgtgttctt ttgcaggtga
     2581 ggtcgtagaa acgccctgag agcctctcag cggtgcacgc aacggatgtt atggtaaatt
     2641 ggtgatctca tcatgctaat tctttctgtg gtaaaatctc tctgagccac ccggttctta
     2701 cataggatat atccatgacc aagtttgaag ctttcaaaga tcagataacg aatgccgcta
     2761 aagcatcttt tcctgagtgg gtaacgtttg aatatgaaaa tgattttcac ggatataatg
     2821 aatcctttgt ttatgaatcc gtctgtgcta ttaaaaaaat gggtgagtta gaagtaagaa
     2881 ataatgcgga cagatatttt agtgtgaagt ttatatcggc ctagcatgtt tgattgtttc
     2941 ggaaagcccg ataaacgtgg gctttcatga atataatcat cagtttttta tgtagttttt
     3001 taattttgct gtttgttcga tggcattagg aatgcagcca aacatattgg cgcaggctgt
     3061 ttgaacgaca atttcgtgcc tttcccctcc aattggagtt tttaccactt gatatcctaa
     3121 aattgcacta ttaccaatag gtgagtacgt tgcaataacc gtttcatccg ccatttgtat
     3181 tttccagcct gaattcattg ctatccaagc ttttgcttta gtccagtaag catcacattg
     3241 ctgcttattt tcgcaatata taggcgcttg agcttgagct gctacttgtg ggctgacatt
     3301 ttgagcgcag ccggtcaagc caaagactcc gagtaataat agagaagtta tttttttcat
     3361 tttaagcctc tgttgtttat ttttttatgt gctgatttta acattatcta tacgtaggaa
     3421 agaagaaagt aggtgtggtt aggttgcaaa agaaaaatga tcttcttgag atccttttga
     3481 gcagcgcgta atctcctgct ctgtaaacga aaaaaccgcc ttgcagggcg gtttttcgaa
     3541 ggttctctga gagatcaact ctttgaaccg aggtaactgg cttggaggag cgcagtcacc
     3601 aaatctgtcc ttccagttta gccttaaccg gcccataact tcaagactaa ctcctctaaa
     3661 cagttatcag tggctgctgc cagtggcgcg ttgtcgtgtc tttccgggtt ggactcaagt
     3721 cgatagttac cggacaaggc gcagcggtcg gactgaacgg ggggggttcg tgcatacagt
     3781 ccagcttgga gcgaactgcc tacccggaac tgagtgtcag gcgtggaatg agataaacgc
     3841 ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga gcgcacgagg
     3901 gagccaccag ggggaaacgc ctggtatctt taagtcctgt cgggtttcgc caccactgat
     3961 ttgagcgtca gatttcgtga tgcttgtcag gggggcggag cctatggaaa aacggcttcg
     4021 ccgtggcctt cttgcttccc tgttaagctt cttcctggaa gatgccagga aatttccgcc
     4081 ccgccagtaa gccggtaccg ctcgccgcag ccgaacgacc gagcggagcg agtcagtgag
     4141 cgaggaagcg gaatatctcc gggcttatct ttggcaccgt acgcgccata gctgcatttt
     4201 tttatacgat gcaggatagg gctaacgccg caaaatgacg tcatccgaca tcattccgcc
     4261 gcgttcgccc agtgacctac agtcggctct ggggtgtcgg ggctgtgccc tgaccaggcg
     4321 ttttggagta tcgccaccgt ggtggcggtg ctacaaaaca tatcctgtcc cttccttggc
     4381 atctctgaag tttagcctgt atacactccg ctagcgctac gtgactggtt cagggctgcg
     4441 ccccgacacc cgctaaaagc actgacgcgc ctgcggcttg cccaaccccg cgccgtccgg
     4501 gaaagaattt cccgatcgac ccgacgtttc tgtttacctg tgatgttaac gtttggatct
     4561 ttttcccggg tttacctatt ttcttctaat gaagcgttca cagctgacgt taatagatgg
     4621 gtgcttcatg tttggttttt caccaggaga acttatgagc ctttgccccg atgaacgtct
     4681 gctctttgtg cggatgattt ccgctatgct tcgccgttcg ggcggtgatg cgggtgctgt
     4741 tatgtttgag gcgtatcgcc atattgtgtc cgataccaat caagctcgtc gttcctacat
     4801 gctcgacctg ctcgaaagcg tcaggcatga ctatgtacac ggtggatata catagttgcc
     4861 ctggatacgc ttttcgtcta agtgagcgtt cttttcgtct ctttattcgc cgtcctgtat
     4921 accgaagcgt gcgctcagct tctgataaag cgcttctgcc tgttcgtgca ttcgctcaca
     4981 gtcggctgcc tcgtcatcaa gatcgagcac gtcgagtttt tcgagcagca gcagcgactg
     5041 cgcccggata aattttgcca tgttcagtgc ggctgattcc tgttttgtca tacggctttt
     5101 tcccggtttt atggtgatcg cagactgaaa tcttacttca ttcacttgag tgcatagcca
     5161 tgcaggtacg cagaaatcat cagcgcgttt ctgagcggtt ttcagggggt aagatgtgtt
     5221 cttttgcagg tgaggtcgta gaaacgccct gagagcctct cagcggtgca cgcaacggat
     5281 gttatggtaa attggtgatc tcatcatgc
//
