LOCUS       NZ_CP124818             6036 bp    DNA     circular CON 14-MAY-2024
DEFINITION  Citrobacter freundii strain CF12 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP124818
VERSION     NZ_CP124818.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14640084
            Assembly: GCF_030007575.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 6036)
  AUTHORS   Fernandez-Calvet,A., Toribio-Celestino,L., Alonso-del Valle,A.,
            Sastre-Dominguez,J., Valdes-Chiara,P., DelaFuente,J. and San
            Millan,A.
  TITLE     The distribution of fitness effects of plasmid pOXA-48 in clinical
            enterobacteria
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6036)
  AUTHORS   Toribio-Celestino,L. and San Millan,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-APR-2023) Microbial Biotechnology, Centro Nacional de
            Biotecnologia-CSIC, Darwin, 3, Madrid 28049, Spain
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina HiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030007575.1-RS_2024_05_14
            Annotation Date                   :: 05/14/2024 05:08:35
            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)                     :: 5,085
            CDSs (total)                      :: 4,966
            Genes (coding)                    :: 4,877
            CDSs (with protein)               :: 4,877
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 89
            CDSs (without protein)            :: 89
            Pseudo Genes (ambiguous residues) :: 0 of 89
            Pseudo Genes (frameshifted)       :: 22 of 89
            Pseudo Genes (incomplete)         :: 61 of 89
            Pseudo Genes (internal stop)      :: 19 of 89
            Pseudo Genes (multiple problems)  :: 11 of 89
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124818.1.
            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..6036
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CF12"
                     /isolation_source="Human gut"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="unnamed4"
                     /geo_loc_name="Spain"
                     /lat_lon="40.416500 N 3.702560 W"
                     /collection_date="2014-10-31"
                     /collected_by="Ramon y Cajal Health Research Institute
                     (IRYCIS)"
     gene            77..892
                     /gene="sul2"
                     /locus_tag="QLG15_RS25390"
                     /old_locus_tag="QLG15_25400"
     ARG             78..889
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            979..>1221
                     /gene="glmM"
                     /locus_tag="QLG15_RS25395"
                     /old_locus_tag="QLG15_25405"
                     /pseudo=""
     CDS             979..>1221
                     /gene="glmM"
                     /locus_tag="QLG15_RS25395"
                     /old_locus_tag="QLG15_25405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008891390.1"
                     /note="catalyzes the conversion of glucosamine-6-phosphate
                     to glucosamine-1-phosphate; 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="phosphoglucosamine mutase"
                     /name="glmM"
     gene            complement(1457..2950)
                     /locus_tag="QLG15_RS25400"
                     /old_locus_tag="QLG15_25410"
     CDS             complement(1457..2950)
                     /locus_tag="QLG15_RS25400"
                     /old_locus_tag="QLG15_25410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISVsa3 family transposase"
                     /protein_id="WP_001120888.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFASRPEIMGWVLGIVYRVIATHLVKKAGH
                     THQVAKTGAVTLIQRFGSALNLNVHFHMLFLDGVYVEQSHGSARFRWVKAPTSPELTQL
                     THTIAHRVGRYLERQGLLERDVENSYLASDAVDDDPMTPLLGHSITYRIAVGSQAGRKV
                     FTLQTLPTSGDPFGDGIGKVAGSSLHAGVAARADERKKLERLCRYISRPAVSEKRLSLT
                     RGGNVRYQLKTPYRDGTTHVIFEPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALV
                     TPAKRGRGNKVRVADEPATPAQRRASMTWAQRLKRVFNIDIETCSGCGGAMKVIACIED
                     PIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLFD"
                     /name="IS91-like element ISVsa3 family transposase"
     gene            complement(2994..3383)
                     /locus_tag="QLG15_RS25405"
                     /old_locus_tag="QLG15_25415"
     CDS             complement(2994..3383)
                     /locus_tag="QLG15_RS25405"
                     /old_locus_tag="QLG15_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            3601..4041
                     /locus_tag="QLG15_RS25410"
                     /old_locus_tag="QLG15_25420"
     CDS             3601..4041
                     /locus_tag="QLG15_RS25410"
                     /old_locus_tag="QLG15_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(4775..4924)
                     /locus_tag="QLG15_RS25415"
                     /old_locus_tag="QLG15_25425"
     CDS             complement(4775..4924)
                     /locus_tag="QLG15_RS25415"
                     /old_locus_tag="QLG15_25425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            5495..5653
                     /locus_tag="QLG15_RS25440"
     CDS             5495..5653
                     /locus_tag="QLG15_RS25440"
                     /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_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     Typing          complement(4960..5133)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5057..5662
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctcgcctggg gattcccttt cgacccgagc atccgtatga gactcatgct cgattattat
       61 tattatagaa gcccccatga ataaatcgct catcattttc ggcatcgtca acataacctc
      121 ggacagtttc tccgatggag gccggtatct ggcgccagac gcagccattg cgcaggcgcg
      181 taagctgatg gccgaggggg cagatgtgat cgacctcggt ccggcatcca gcaatcccga
      241 cgccgcgcct gtttcgtccg acacagaaat cgcgcgtatc gcgccggtgc tggacgcgct
      301 caaggcagat ggcattcccg tctcgctcga cagttatcaa cccgcgacgc aagcctatgc
      361 cttgtcgcgt ggtgtggcct atctcaatga tattcgcggt tttccagacg ctgcgttcta
      421 tccgcaattg gcgaaatcat ctgccaaact cgtcgttatg cattcggtgc aagacgggca
      481 ggcagatcgg cgcgaggcac ccgctggcga catcatggat cacattgcgg cgttctttga
      541 cgcgcgcatc gcggcgctga cgggtgccgg tatcaaacgc aaccgccttg tccttgatcc
      601 cggcatgggg ttttttctgg gggctgctcc cgaaacctcg ctctcggtgc tggcgcggtt
      661 cgatgaattg cggctgcgct tcgatttgcc ggtgcttctg tctgtttcgc gcaaatcctt
      721 tctgcgcgcg ctcacaggcc gtggtccggg ggatgtcggg gccgcgacac tcgctgcaga
      781 gcttgccgcc gccgcaggtg gagctgactt catccgcaca cacgagccgc gccccttgcg
      841 cgacgggctg gcggtattgg cggcgctgaa agaaaccgca agaattcgtt aactgcacat
      901 tcgggatatt tctctatatt cgcggttcag caggcatgtc ccctttgagg gcgacccgac
      961 gacaggataa tcgaccttat ggtgcgcaaa tatttcggca cagacggtat tcgtggcaaa
     1021 gccaacgaag gcgcgatgac ggcggaaacc gccttgcgcg tcggcatggc ggctggccgt
     1081 gtctttcgtc gcggtgacca ccgccatcgt gtcgtgatcg gcaaggatac gcgcctgtcg
     1141 ggctatatgc ttgaacccgc gctcacagcc ggtttcacct cgatgggcat ggacgtattc
     1201 ctttttggcc cgctgccgac aacgtatagg aagaataaac gcccttttca cccaagtcca
     1261 acagctttgg accgcagttg actctttcga cacccctgcg atgcaaccca atccggctga
     1321 cggggagcca gcaacgctga aaatttaccc tcctctttcc cactagcggc tccttttccg
     1381 acaaccagca cggcggatcc ctgccgcggc gctgtgaacg cagcattttg attggtatcg
     1441 ttggccttca ggctcgtcag tcaaacagac ccaggagcag ctcagccggt ggcgcccggc
     1501 tttcgggtaa cgccctggtc ccgctggttt cggctttgtg cttcaggtga tcaaggatct
     1561 gcttgatcac tatagggtct tcaatgcagg cgatgacttt catggcgccg ccgcagccgc
     1621 tgcaggtctc gatgtcgata ttgaaaacac gcttgagccg ttgcgcccat gtcatcgacg
     1681 ctcgccgttg tgctggtgtt gccggttcat cagccaccct gaccttgttg cccctgcccc
     1741 gttttgccgg cgtgaccaac gcccggtgcc gactgttggg tgcgaacacc ccgtggaagc
     1801 gggttaggtt gactctgggc ttcggtacca gggcggccag ccttgcaatg aaatccaatg
     1861 gttcgaaaat gacgtgcgtg gtgccgtccc ggtacggcgt cttgagctgg tagcgcacgt
     1921 tgccgcctcg tgttaacgac agccgcttct cggataccgc cgggcggctg atgtaccggc
     1981 acagccgttc gagcttcttg cgttcatcgg ccctggccgc cacgccggcg tgcaggctgg
     2041 acccggctac cttgccaatc ccgtcaccga acggatcacc actggtcggc agagtttgca
     2101 aagtgaacac ctttcgcccc gcctgtgaac cgacagcgat acggtaagtg atcgagtgcc
     2161 ccagcagggg tgtcatcggg tcgtcatcca ccgcatccga ggccagatag ctgttttcga
     2221 catcccgttc cagcaggcct tgccgttcca gatagcgacc cacccggtgg gcgatggtgt
     2281 gcgtcagctg ggtgagctct gggctggtcg gcgccttgac ccagcggaaa cgcgctgagc
     2341 cgtgggattg ctcgacatac acaccgtcga gaaacagcat gtggaagtga acattcagat
     2401 tgagcgccga tccaaaacgc tggatcaggg tgaccgcgcc cgtcttggcc acttggtggg
     2461 tatggcccgc tttcttgacc aggtgcgtgg caatgacgcg gtaaacgatg cccagcaccc
     2521 accccatgat ctcgggccgg ctggcaaaca ggaaacgcag ctgaaacggg aagctcaaca
     2581 cccactgacg catgggttgt tcaggcagta cttcatcaac cagcaaggcg gcactttcgg
     2641 ccatccgccg cgccccacag ctcgggcaga aaccgcgacg cttacagctg aaagcgacca
     2701 ggtgctcggc gtggcaagac tcgcagcgaa cccgtagaaa gccatgctcc agccgcccgc
     2761 attggagaaa ttcttcaaat tcccgttgca catagcccgg caattccttt ccctgctctg
     2821 ccataagcgc agcgaatgcc gggtaatact cgtcaacgat ctgatagaga agggtttgct
     2881 cgggtcggtg gctctggtaa cgaccagtat cccgatcccg gctggccgtc ctggccgcca
     2941 catgaggcat gttccgcgtc cttgcaatac tgtgtttaca tacagtctat cgcttagcgg
     3001 aaagttcttt taccctcagc cgaaatgcct gccgttgcta gacattgcca gccagtgccc
     3061 gtcactccca ctcttacatt gttcgcagta tctaggtaca tgttattgcg tgcaccttca
     3121 tgatgtataa tgttattaat gacagcagaa agatcgacag aattaatatt cttcgtacct
     3181 gggacagtta tcgggtgtcg gccagtgatg agaccaaagg atgcagtata agatgaacca
     3241 ctactattat catggccacc attaccacca ccgttaaaac tacctcccga acttccagag
     3301 ccgctatgac catcattgta ggggtcattt ggtcccatgt gaccaaaacc accgacagta
     3361 ccgctattta actctgtact cataaaatta tcctctttga cttttaaaaa cagcaaaaac
     3421 tgtatttata acaatgtgtt tatatacagt attcgaaata ctacgcccgt caaaaccaca
     3481 ccgtcaacag gttttttgtg tatttttcac gcctcacggg cagcctcaga ccttttgtgt
     3541 taaaacagta atatgttctg ctgttacaat acggtacaca caggagacac tgtcactttt
     3601 atggcatggc acacagttca agagacactg aaattaacag gaaagtcgcg ctcgcaatta
     3661 tatcgtgaca tggctaaagg ccttgtcagc tatcgcacag gaaaaaatga tcgccgggag
     3721 ttcgagacca gtgaactgat tcgggcctat ggcgagctgc gcacttctga gacaccaaaa
     3781 aggcacaagg agggacactc caaatctgtc gttagccagg cggaaaatgc tcagctagac
     3841 gtcattcagc agaaactgga cgctctgcag cagactgtta ccctaatgct tgaagacaag
     3901 atggcgcggg aagcagaaaa ccgcctgcga aatgaggaga gggaacaact acaggccgaa
     3961 attagccgtc tggctgacgc gctggcacag gaaaaaaagc ggggattctg gtcgcggctg
     4021 tttcgctccg gttcagagta acagtgcagg tgactctgat ttaccataac atctgttatc
     4081 agcaccgcct gagaggccct cagggcgttt ctgacgggaa accggtaaaa caggcaacaa
     4141 accacccgaa aacccgccag aaacgcgcag gctctgtttt tacggcatgc atgagtatgc
     4201 gcacaagtgc atagcgcgga aattcacacc attcagccgg ggtaagtcct gtttccggcg
     4261 ttcttcccat ccgaaaacgg tgaacgggga cgcaatttat tgcgtggccg tgaagcgttg
     4321 ccggcgcagc cggaaaaccc gctgtcagca cgttcaggaa gggggtgatg tacaaatggc
     4381 acagaggatg aaagtgacgt atgagctgaa ggaatgatgt aaaagtgatg taaaagtgat
     4441 gtatgaactg aaggagcgat gtaattctgt agtcaggaag aataacccgt tcatgcaggc
     4501 atgaacgata cagtgaggaa cgcttttttt gtcacgatct ccccttaacc tgcgtaaatc
     4561 acccgccatg gttgattatt tttcaacctc aaaatggtca tacacctaac gcagccgcga
     4621 ttttcatcgc aactgcatga attaaaagaa aaaaaaggaa tatttcgttt tcacgagtaa
     4681 tacccgggta ttaaaaatcc actgtaatta catgaaaata aagaaataaa aggtaatacc
     4741 ggagtattac cacgtacgcg ggcaagcgaa aaagctataa cgcttcccgg ccgacaggcg
     4801 acccaaaatc cacaggggca tgcaggttct cttcagtaac ctgcgccatt aaatcaaaaa
     4861 ggtcatattc gccgggaagc tgcgtatcag tcgaatccag ttgttcatca tattcagatg
     4921 gcatggggtg atatccagta gctgagaggt tgttagcggg tttcggggcg cagccctgaa
     4981 ccagtcatgt agcgctagcg gagtgtatac tggcttacta tgttgccacg attgcgaaaa
     5041 tcagtgaagt gcttcatgtg gcaggagaaa aaaggcagca ccggcgcgtc agcagaatat
     5101 gcgatacagg agatattccg cttcctcgct cactgactcg ctacgctcgg tcgttcggct
     5161 gcggcgagcg gtaccggctt acggacgggg acggaaattt cctggaagat accaggaaga
     5221 cacttagcaa agaagagata aggccacggc gaagccgttt ttccataggc tccgcccccc
     5281 tgacaagcat cgcaaaatct gacgctcaaa tcagtggtgg cgaaacccga caggactata
     5341 aagatcccag gcgtttcccc ctggtagctc cctcgtgcgc tctcctgttc ctgcctttcg
     5401 gtttaccggt gtcattccgc tgttatggcc gcggtttctc attccacgcc tgacactcag
     5461 ttccgtgaag gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga
     5521 ccgctgcgcc ttgtccggta actatcaact tgagtccaac ccggaaagac acgacaaaac
     5581 gccactggca gcagccatta gtaacaggag tgcacgagaa gatagattaa gaggtcttga
     5641 agtagaggcc tgactgcggc tacactgaaa gaacagtttt ggtaatggcg gtctcgtgaa
     5701 ccctgttacc gggttaagca gttccccaac tgacttaacc ttcgaacaaa ccgcctcccc
     5761 aggcggtttt ttcgtttaca gagcaagaga ttacgattca ttgaaaagga tctcaagaag
     5821 atcctttgta gattactatc aattaatctt ccgaacatga caccagtcac tgttgattac
     5881 ggttaaaccg ctccgtaaca ggtttccctc gtattggtga cttgcagcac caaagaagca
     5941 aaaaagataa atatatctac ttattgagag atgatatatt tatttccaaa atgctacaga
     6001 tacatcatca tgaaacggat caccgcaaac aggtta
//
