LOCUS       NZ_CP011607             4938 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter freundii strain CAV1321 plasmid pCAV1321-4938, complete
            sequence.
ACCESSION   NZ_CP011607
VERSION     NZ_CP011607.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03733741
            Assembly: GCF_001022155.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4938)
  AUTHORS   Sheppard,A.E., Stoesser,N., Wilson,D., Sebra,R., Kasarskis,A.,
            Anson,L., Giess,A., Pankhurst,L., Vaughan,A., Grim,C.J., Cox,H.,
            Yeh,A., Sifri,C.D., Walker,S., Peto,T.E., Crook,D.W. and
            Mathers,A.J.
  TITLE     Rapid spread of a carbapenem resistance gene driven by multiple
            levels of genetic mobility
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4938)
  AUTHORS   Sheppard,A.E., Stoesser,N., Wilson,D., Sebra,R., Kasarskis,A.,
            Anson,L., Giess,A., Pankhurst,L., Vaughan,A., Grim,C.J., Cox,H.,
            Yeh,A., Sifri,C.D., Walker,S., Peto,T.E., Crook,D.W. and
            Mathers,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUN-2015) University of Oxford, John Radcliffe
            Hospital, Oxford OX39DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP3 v. 2.3.0
            Genome Coverage                   :: 115X
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001022155.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 02:09:54
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,394
            CDSs (total)                      :: 5,273
            Genes (coding)                    :: 5,156
            CDSs (with protein)               :: 5,156
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 29 of 117
            Pseudo Genes (incomplete)         :: 83 of 117
            Pseudo Genes (internal stop)      :: 19 of 117
            Pseudo Genes (multiple problems)  :: 14 of 117
            Pseudo Genes (short protein)      :: 1 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011607.1.
            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..4938
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CAV1321"
                     /isolation_source="Urine/Genitourinary"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCAV1321-4938"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2010-11"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            238..453
                     /locus_tag="AB180_RS28110"
                     /old_locus_tag="AB180_00085"
     CDS             238..453
                     /locus_tag="AB180_RS28110"
                     /old_locus_tag="AB180_00085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            929..2047
                     /locus_tag="AB180_RS00085"
                     /old_locus_tag="AB180_00090"
     CDS             929..2047
                     /locus_tag="AB180_RS00085"
                     /old_locus_tag="AB180_00090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012402750.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA methyltransferase"
                     /protein_id="WP_080917352.1"
                     /translation="MSLAPGVVRDSIIECFLRLGREASIEEITKAVYLKIGKISKSSVR
                     SYLSLNTPGLFERVDRGVYRLNGDAGITPSLDLTSSPKTVGKSTIFFDDAIEWLKRQKD
                     NSIHAVVTDPPYGLVEYTKQQTEKLRAGKGGIWRKPPSFDGHKRAPLPRFTVLREEDLR
                     NISLFFKELSSQVERVVVPGGNIVIASNPLLSHIVADSMSTSGLELRGYIVRQVMTMRG
                     GDRPKNAHDEFGDVSVMPRSQWEPWIVLRKPLDGRVQDNLRKWKTGGFRRISADRPFGD
                     VIKSHPTPAHEKKIAPHPSLKPQNFMRQLVRAVLPLGEGIILDPFMGGGSTLAAANHIG
                     YESIGVEIDREFFDLAEKAIPALSALPSKENN"
                     /name="DNA methyltransferase"
     gene            complement(2044..2649)
                     /locus_tag="AB180_RS00090"
                     /old_locus_tag="AB180_00095"
     CDS             complement(2044..2649)
                     /locus_tag="AB180_RS00090"
                     /old_locus_tag="AB180_00095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006338602.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047715645.1"
                     /translation="MQDRSVVNRQGFNPEIDLPYSLRISDFEHAMEDIYDFFHDVNNLL
                     SNKGLHRLDDMMRPAAMSGLISDMITASLAKFSRSLVENKHFNGHPDLVVRGRYPNDSI
                     SSGEEGIEIKTTRKNGGAVDTHGARSQWMCVFVYNVDNETEPASDRKSMKFTEVYLCHV
                     DENDFRRNDRGALGTRTATLHKEGLKKLRESWVYKDLV"
                     /name="hypothetical protein"
     gene            complement(2916..3029)
                     /locus_tag="AB180_RS26580"
     CDS             complement(2916..3029)
                     /locus_tag="AB180_RS26580"
                     /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_032634168.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            3653..3994
                     /locus_tag="AB180_RS00095"
                     /old_locus_tag="AB180_00100"
     CDS             3653..3994
                     /locus_tag="AB180_RS00095"
                     /old_locus_tag="AB180_00100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4203..>4631
                     /locus_tag="AB180_RS28975"
                     /pseudo=""
     CDS             4203..>4631
                     /locus_tag="AB180_RS28975"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          3384..3559
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="81.215"
                     /coverage="100.0"
                     /evalue="3.58e-30"
     Typing          complement(2917..3436)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.587"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4..569
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.413"
                     /coverage="99.0"
                     /evalue="1.7e-108"
     Typing          3985..4937
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gccagcctga gcggggtgct gtggtaccag gggaaccgga tagcggcgaa cctggcggaa
       61 atcaggcagc agagagatac gctgtcgaaa ctgcagatgc agacgtgggg cgtgacctat
      121 ctggagaacc gcaacggacg gtttctggtg ctgccggagg ggatgaaagc cgaaacgggc
      181 cggacggtgg acaacaagac gcggaacgcg gtgaagctgg tacgggagta gagcagaatg
      241 acggaactgg aaaaacaatt gctgagcgcg ttagagcagc tacagcagga ctactcgaga
      301 aggctggacg agtgggagag cgccttcgag gaatggcgga agatgtctgg tcttatgcaa
      361 cgggagaacg cggcgctgag cgagcgcgtg tcgggcttga gcaggcaggt gcagagtttg
      421 agcgagcagc tgcgccggtt atcgacaggc tgaatgagat tgatcaacag cgatacgggc
      481 aaagaacgga aaaggaacca gagaagacag cagatctggt accggaacgg caacgcacat
      541 tatctcatgg tgacagggag tatggagact gataaacgcc cgtctcaggt ggcctgagcg
      601 tgacggggat catggccatt ttctgcgatt tcagcacaca gagagtcttt tttaaccgaa
      661 atcaccggct atgcagtgat gtgaataagt gatgcatatg cgtaaaataa atcaggtgcg
      721 tttctggtgg ttttcggtgt acttgccacc accttttgcc cgtcagccat cagaaacgcc
      781 ctgagggcct ccggcgcggt gcgggtaagg gatgttatgg taaaaaaaaa gttaatgtat
      841 acttttttga cgtctctttt aaactaaatt gacgtcctga cgtctagtta gtattattat
      901 tttatataaa aatactggat ttataaacat gtctttggct cctggtgttg ttcgtgactc
      961 gataattgaa tgttttttaa ggcttggaag agaagcttct attgaggaga taacaaaagc
     1021 tgtttattta aaaattggaa aaatttcaaa gtcttctgtt cgctcatatc tgagtttaaa
     1081 taccccaggt ctgttcgagc gagtagaccg aggtgtctat cgcttaaatg gtgatgctgg
     1141 tattactccc tccctagatt tgacgtcttc acctaagacg gttgggaaat cgacgatttt
     1201 ttttgacgat gcaattgaat ggttaaaaag acaaaaagat aattcaattc atgcagttgt
     1261 aactgatcct ccttacggat tagtcgagta tacaaaacaa cagactgaga aactaagggc
     1321 agggaaaggt ggtatttgga gaaagccacc ttcctttgat ggacataagc gagcgccatt
     1381 acctcgcttt acggttttgc gggaagaaga cctcagaaat atatcattat ttttcaaaga
     1441 actatcctcg caagtcgaaa gggtggttgt tcctggcggg aatatagtta tcgcatccaa
     1501 ccctctacta tcccatatag tcgcggactc tatgtctacg tctggcttag agctacgagg
     1561 ttacattgta cgtcaggtta tgaccatgag aggtggggat agacccaaaa acgcccatga
     1621 tgaatttgga gatgtttctg tcatgcctcg ttctcaatgg gaaccatgga tagtgttgag
     1681 aaagcctcta gatggaaggg ttcaggataa tctaagaaag tggaaaacag gtggattcag
     1741 gaggatttca gctgataggc catttggcga cgtcatcaaa tctcatccga cgccagcaca
     1801 cgaaaaaaag atagcgccac atccctcatt aaagccgcaa aatttcatgc gacaattagt
     1861 gagggcagtg cttcctttgg gagaggggat tattctcgat ccatttatgg ggggaggctc
     1921 cacattggca gctgcaaatc atataggtta tgagagcatt ggagttgaaa tagaccgaga
     1981 gttctttgat ttggcggaga aggctatccc cgcgctatca gctcttccta gcaaggaaaa
     2041 taactaaact aagtccttgt aaacccagct ttctctgagc ttcttcaacc cttctttgtg
     2101 aagggttgct gttctggttc ctaatgcacc acgatcatta cgacggaagt cattttcatc
     2161 aacgtggcaa agatatacct cggtaaattt catcgacttt ctgtctgagg ccggttcggt
     2221 ctcattatcg acattgtaga caaatacgca catccattga gatctggccc cgtgagtatc
     2281 gactgccccc ccatttttcc gggtggtttt tatttcaatg ccttcttctc ctgaggagat
     2341 actgtcattc ggatacctgc ccctaacaac taggtctgga tgtccattga aatgcttgtt
     2401 ttcaacaagc gatcttgaaa atttagcgag ggaagctgtg atcatatctg atatgaggcc
     2461 agacatagct gctggtctca tcatgtcatc aagcctatgc aaacctttgt ttgatagtaa
     2521 gttgttcaca tcatggaaga agtcataaat atcttccatc gcgtgctcaa aatcactaat
     2581 ccttagcgaa tacggcagat cgatctctgg gttaaatccc tgtcgattaa ctactgacct
     2641 gtcttgcatc ttagttcctt gaataagata taaaagttcg aaagctcttt gtcatatctt
     2701 accaagaaga tccttgacga tcattgtcgt ttgggcgtag cctcttgaaa cgaaaaaacc
     2761 gcctggggag gcggtttaat cgaaggttaa gtcagttggg gaactgctta accaggtaac
     2821 tggcttggtg gagcgcagat accaaatact gtccttccag tgtagccgca gtcaggtcac
     2881 cacttcaaga actctcaata tctaaatcca ccttttcagt taccagtggc tgctgccagt
     2941 ggcgcttttg catgtctttc cgggttggac tcaagacgat agttaccgga taaggcgcag
     3001 cagtcggact gaacgggggg ttcgtgcata cagtccagct tggagcgaac tgcctacccg
     3061 gaactgagtg tcaggcgtgg aatgagacaa acgcggccat aacagcggaa tgacaccggt
     3121 aaaccgaaag gcaggaacag gagagcgcac gagggagcta ccagggggaa acgcctggga
     3181 tctttatagt cctgtcgggt ttcgccacca ctgatttgag catcagattc tgtgatgctc
     3241 gtcagggggg cggagcctat ggaaaaacgg caacgccgca tccttttttc tggccttcct
     3301 gacgtgagcg ctatttcttt ctctcgtcac tcgtgagctg gtaacgcccg ccgcagtctc
     3361 acggcaggag cgcagcgacc gagtgagcga ggaggcgtca tacccccggc actaccatta
     3421 tctgccttac gcaccgtcgc tgcatgtcat ccctgccata tatagcactt tcgctgatac
     3481 ccataccgat gccaccatag taagccagta tacactccgc tagcgctacg tgactggttc
     3541 agggctgcgc cccgaaaccc gctaaaaacc actgacgcgc ctgcggcttg tccaaccccg
     3601 cgccgaccgg gaaaggcttt cccgtccgtc acggggttat caggaggcga ttctggcaga
     3661 taaacgcaac aagatgctca cgatgtgggt gacggaagac gaacaccggc ggttgcttga
     3721 gcggtgcgac ggaaaacaac tggcggcgtg gatgcgccag acctgccttg atgagaaacc
     3781 gacacgcgcc ggcaggctcc cctcgatttc gccggcgctg ctgcgtcagc ttgctggcat
     3841 gggcaataac ctgaaccaga tcgcccggaa agtgaacgcc ggtggtgccg gtcatgaccg
     3901 ggtgcagatc gtggcagcgc tgatggcgat cgatgccggt ctggaacggt tgcggcatgc
     3961 cgtactggaa aaagggccgg acgatgattg ttaaattcca tccacggggt cgcggcgggg
     4021 gagccggtcc ggtggactat cttctgggta aagaccggca gcgtgaaggt gccagcgtcc
     4081 tgcaggggaa gccggaagaa gtccgggagc tgattgatgc gtcgccgtat gtgaaaaaat
     4141 atacctccgg ggtgctgtca ttcgcggagg cggacctgcc gccgggtcag cgtgaaaaac
     4201 tgatggccag ctttgagcgg gttctgatgc ccggactcga taaagatcag tacagcattc
     4261 tgtgggtgga acacgcagac aagggtcgtc ttgagctgaa ttttctgatc cccaataccg
     4321 aattactgac ggggaaacgc ctccagccgt attacgatcg tgccgaccgg ccgcgcatcg
     4381 atgcgtggca gacagtggtc aacggcaggc tggggctaca tgatccgaac gacccggaga
     4441 accggcgggc gctggtcacg ccgtcaggac tgccagaaac gaagcaggaa gccgcggaga
     4501 cgattacacg gggtttgctg atgttagcct catcaggaga gctgaaaacg cgtgatgacg
     4561 tcacaggggc gctcacagcg gccggttttg aggtggtcag aaccacaaaa aacagtatca
     4621 gcattgccga cccggacggg gggcgaaata tccgactgag gggagccatt tatgagcagt
     4681 cttttaacgg cctcgaggga cttcgaggag aaatcgaaag cacagcagca gcttaccgaa
     4741 gagaggctga aagccgcatt cagcaagcac gagaacgttg tcaaatcgga actgaacgca
     4801 agcgcgaaga gaatcaacga cgccatcagc gcccacgaac aggggatgaa cgcggcgatg
     4861 cagtcgaacc ggctgagcgt gctgcgaatg gtcgggcgga cgtggctgac catcaccatg
     4921 gtgtcagggc tgctgttc
//
