LOCUS       NZ_CP104924             5113 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Citrobacter portucalensis strain AHM21C2861I plasmid pHNAH212861-2,
            complete sequence.
ACCESSION   NZ_CP104924
VERSION     NZ_CP104924.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30685708
            Assembly: GCF_030169875.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter portucalensis
  ORGANISM  Citrobacter portucalensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5113)
  AUTHORS   He,W., Gao,M., Lv,L., Wang,J., Cai,Z., Bai,Y., Gao,X., Gao,G.,
            Pu,W., Jiao,Y., Wan,M., Song,Q., Chen,S. and Liu,J.H.
  TITLE     Persistence and molecular epidemiology of blaNDM-positive
            Gram-negative bacteria in three broiler farms: A longitudinal study
            (2015-2021)
  JOURNAL   J Hazard Mater 446, 130725 (2023)
   PUBMED   36630875
REFERENCE   2  (bases 1 to 5113)
  AUTHORS   He,W., Gao,M., Lv,L. and Liu,J.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2022) College of Veterinary Medicine, South China
            Agricultural University, Wushan, Tianhe District, Guangzhou,
            Guangdong 510642, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030169875.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 05:20:09
            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)                     :: 5,149
            CDSs (total)                      :: 5,032
            Genes (coding)                    :: 4,927
            CDSs (with protein)               :: 4,927
            Genes (RNA)                       :: 117
            rRNAs                             :: 10, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 10, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 105
            CDSs (without protein)            :: 105
            Pseudo Genes (ambiguous residues) :: 0 of 105
            Pseudo Genes (frameshifted)       :: 33 of 105
            Pseudo Genes (incomplete)         :: 74 of 105
            Pseudo Genes (internal stop)      :: 17 of 105
            Pseudo Genes (multiple problems)  :: 17 of 105
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104924.1.
            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..5113
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="AHM21C2861I"
                     /isolation_source="In-house environment"
                     /db_xref="taxon:1639133"
                     /plasmid="pHNAH212861-2"
                     /geo_loc_name="China"
                     /collection_date="2021-05"
     gene            complement(45..176)
                     /locus_tag="N5860_RS25785"
     CDS             complement(45..176)
                     /locus_tag="N5860_RS25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /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_082196965.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPEKHDKAPLAAAIGRGCTRDY"
                     /name="replication initiation protein"
     gene            824..1147
                     /locus_tag="N5860_RS25715"
                     /old_locus_tag="N5860_25710"
     CDS             824..1147
                     /locus_tag="N5860_RS25715"
                     /old_locus_tag="N5860_25710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_126289757.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1356..>1790
                     /locus_tag="N5860_RS25720"
                     /old_locus_tag="N5860_25715"
                     /pseudo=""
     CDS             1356..>1790
                     /locus_tag="N5860_RS25720"
                     /old_locus_tag="N5860_25715"
                     /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"
     gene            1825..2316
                     /locus_tag="N5860_RS25725"
                     /old_locus_tag="N5860_25720"
     CDS             1825..2316
                     /locus_tag="N5860_RS25725"
                     /old_locus_tag="N5860_25720"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_048237138.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSLLRTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            2323..2538
                     /locus_tag="N5860_RS25730"
                     /old_locus_tag="N5860_25725"
     CDS             2323..2538
                     /locus_tag="N5860_RS25730"
                     /old_locus_tag="N5860_25725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3275..3811
                     /locus_tag="N5860_RS25735"
                     /old_locus_tag="N5860_25730"
     CDS             3275..3811
                     /locus_tag="N5860_RS25735"
                     /old_locus_tag="N5860_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005200081.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_048237141.1"
                     /translation="MFDTDCITVLTARGITEILNSGGSQAWRLDATHVAKLPYLVCVQN
                     SKKDWGSQEAKHHHAFMIGKISGVSRAPENPKRWIINIDSYAEIDIPGQWDGNRNPVSY
                     RKLEDMGIDISKVDFQPLPKEDSLVLNTIKGGDEYDEYEEDSNRVRPINLKEAKAGLAL
                     YFGVNEDDIQITIKG"
                     /name="hypothetical protein"
     gene            3816..4406
                     /locus_tag="N5860_RS25740"
                     /old_locus_tag="N5860_25735"
     CDS             3816..4406
                     /locus_tag="N5860_RS25740"
                     /old_locus_tag="N5860_25735"
                     /inference="COORDINATES: protein motif:HMM:NF019843.4"
                     /GO_function="GO:0005515 - protein binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetratricopeptide repeat protein"
                     /protein_id="WP_053069355.1"
                     /translation="MPSLSVERWLALATAGDSQARFHLGKIFSCGLGVHQDYKQAIYWF
                     QLAAEQGHDDAQFSLGLAYHLGLGGYKDAQKASEWYQKAAEQGHAEAQFQLGRLYTFSD
                     LRNDALAVEWFLCAAKQDHSSAQFKLGWMYHLGMGVEQSDRQAFHWFILAAEQDHAGAQ
                     ASLGEMYKHGWGVEQDDVAAQDWFYRARTMHYP"
                     /name="tetratricopeptide repeat protein"
     gene            complement(4502..4918)
                     /locus_tag="N5860_RS25745"
                     /old_locus_tag="N5860_25740"
     CDS             complement(4502..4918)
                     /locus_tag="N5860_RS25745"
                     /old_locus_tag="N5860_25740"
                     /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_142908665.1"
                     /translation="MTFSITEVREGRIGSLVITKELYDKLEKYSCSNGLITSTYNHGHG
                     VVRYYTVKYCLQMNYHGQNHPQKYLIKRGGRYPSKYSMVKKTVEELEYSTPTFDAICRN
                     IAIKYPHMVKFANYISETPLKGFAATFNNSVDND"
                     /name="hypothetical protein"
     Typing          539..711
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.205"
                     /coverage="100.0"
                     /evalue="4.4699999999999994e-54"
     Typing          complement(9..560)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.682"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          825..1141
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.34"
                     /coverage="99.0"
                     /evalue="8.36e-62"
     Typing          1138..2630
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttccagttta gccgtagttt ggctctaact tcaagaactc tgcatcagta atctcttgta
       61 caccctctac caatggctgc tgccagtggc gctttgtcgt gtttttccgg attggactca
      121 agttgatagt taccggataa ggcgcagcgg tcggactgaa cggggggttc gtgcatacag
      181 tccagcttgg agcgaactgc cttcccggaa ctgagtgtca ggcgtggaat gagacaaacg
      241 cggccataac agcggagtga caccggtaaa ccgaaaggca ggaacaggag agcgcacgag
      301 ggagccgcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccaccactg
      361 atttgagcgt cagattctgt gatgcttgtc aggggggcga agcctatgga aaaacggctc
      421 cgccgtggcc ttctcgcttc cctgttaagt ttcttcctgg catcttccag gaaatttccg
      481 ccccgttcgt aagccatttc cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg
      541 agcgaggaag cggaatatat cctgtatcac atattctgct gacgcgctgg tgccaccttt
      601 ttctcctgct acatgaagca ctttcataaa gtgttactcc gccgtaacat attaagccag
      661 tatacactcc gctagcgctg cgtgactggt tcagggctgc gccccgaaac ccgccaaaag
      721 cctgacgcgc ctgcggcttg tccaaccccg cgccgaccgg gaaagggttt cccgcccgtc
      781 ccggcgttat caggagaccg gtttgtcaga gaaacggaac aagatgctca cgatgtgggt
      841 gaccgaagat gagcaccgcc gtctgctgga acgctgcgac ggtaaacagc tcgcggcctg
      901 gatgcggcag acctgcctgg acgaaaagcc tgcgcgcacc ggaaagctcc cctcaatctc
      961 gccggcgctg ctgcgccagc ttgccggcat gggcaataac ctgaaccaga tagcccgccg
     1021 cgttaacgcc ggcggcggca ccggccatga cagggtacag attgtggcgg cgctgatggc
     1081 catcgatgcc gggcttgagc ggctgcggca cgccgttctt gagaaaggaa cggacgatga
     1141 tcgttaaatt tcatccacgc ggtcgcggcg gtggcgccgg gccggtggac tatctgctgg
     1201 gtaaagaccg gcagcgtgaa ggcgccagcg tcctgcaggg gaagccggac gaagtccggg
     1261 agctgattga cgcgtcgcct tacgtgaaga aatacacctc cggcgtcctg tcgtttgcgg
     1321 aggccgatct gcctcccggc cagcgggaaa aactgatggc cagcttcgag cgggttctga
     1381 tacccggact tgataaagat cagtacagca ttctgtgggt ggagcacgcg gacaaggggc
     1441 gtctggagct gaactttctg atccccaata ccgagctgct gaccggcagg cggctccagc
     1501 cgtactacga cctcgccgac cggccgcgta tcgatgcctg gcagaccatc gtgaacggca
     1561 gactggggct gcacgacccg aacgcgccgg aaaaccgccg ggcgctggtc acgccgtccg
     1621 gactgccgaa aacgaagcag gaggccgcag aagccatcac gcgcggactg ctgatccttg
     1681 cttcgtccgg ggagctgaaa acccgtcagg acgtcactga ggcgctggaa cggtcaggtt
     1741 ttgaggtggt acgcaccacg aaaagcagta tcagcattgc cgacccggac ggggggcgaa
     1801 acatccgact gaagggagcc atctatgagc agtcttttaa cgctggcgaa ggacttagag
     1861 cagcaatcga aagcgcagca gcagagtacc ggcgagatgc tgaaagccgc attcagcgag
     1921 cacgagcagt ctgtcagagc ggaactgagc gcaagcgcga ggagaatcag cgacgccatc
     1981 ctcgcccacg agcagagtat gagcgaggcg atggagaaaa accggcggag cttactgcgg
     2041 actgccgggc ggacatggct caccatcctg atggtgtcag cgctgctgat cggcacgagc
     2101 gggagcatac tgtggtggca ggggcagcag ataaccgaca attacacgca tcttcgtcag
     2161 caggaagata ccctggcgaa aatgaccgcc cggacgtggg gagtgcgcta tcaggagagc
     2221 agcgacggcc ggaggtttct tatcctgccg ccggggatgc aaaccgaagc catcccttac
     2281 gacgggacga catggatccg cctgaaacag gagtagcgga agatgacaga gctggaaaag
     2341 cagttgctga gcgcattaga gcagctacag caggactact cgcaaaggct ggacgaatgg
     2401 gagagcgcct tcgcggaatg gcggagcatg tgtgggctta tgcaacggga gaacgcggtg
     2461 ctgaacgagc gcgtgtcgga cttgagcacg caggtgctga gtttaagcga gcagctgcgc
     2521 cgcttgtccg ggaactgaat gccatcgagc tccggcagag ggagaatgag tatcagaaaa
     2581 cactggagct ggagcgccag ccgcagaaaa cctaccgcgg gccgacactt taaaccatcc
     2641 agacagctga caacccgcac gaagagggac tcttacttct cccgctaaat aggttcgtga
     2701 tcaaaaagat cacggcctat acctgggggg gaattatgaa attgcttaac gtcattgaag
     2761 ctgtacttaa ctgcctgtat ctggcggccg ggctgtggga ctggctggag aagcatttac
     2821 ctgtttttaa ggcgttcgcg ctgattttag tgtgacttta cacgccatgc atctggctgc
     2881 atggctatgc agccgggtaa aatttatctg tcacgaacgg ggcggtgtat cgggtggttt
     2941 gttgccggtt ttacctgact gccgccccgt ttgtggcgaa cccgtccgga gcggtgccga
     3001 caagaactct tatgttaaat gcggcggtgt ggcgggttca tacttcacac atcatgttgt
     3061 cactcagact gagtccagag agaaaaagcc ctccggccga agtcgagtag tgttttactt
     3121 gtttttttgc agttctagga gtaatggtcg tagtagttaa gctagttatt tgtatatatc
     3181 ttgtagttta gtgttgagct cttccgtttt tgatgctaaa aagattgtca ttacgcggtg
     3241 acttgccttt tttaaaacaa aaatggagat atctatgttt gatactgact gcattactgt
     3301 tcttacagct aggggtatta ctgagatttt aaatagtgga ggaagccaag cttggagact
     3361 tgatgctact cacgtagcta agcttccgta cctggtttgc gtccaaaatt cgaaaaaaga
     3421 ctggggtagt caggaggcta agcatcatca tgcatttatg atcgggaaaa tatccggagt
     3481 aagtcgagcc cctgaaaacc ctaagcgctg gatcataaat attgattcct atgctgaaat
     3541 tgatatccct gggcagtggg acggcaatcg taatccagtc tcctatagaa aacttgaaga
     3601 catgggaatt gatatctcta aagtggattt ccaaccccta cctaaagagg attccttagt
     3661 cttgaatacg ataaaaggcg gggatgaata tgatgagtat gaggaggata gcaacagagt
     3721 taggccgata aatctaaaag aggctaaagc agggttggct ttatattttg gtgtgaatga
     3781 ggatgatatt cagatcacaa ttaagggatg accttatgcc gtcactctct gttgagcgct
     3841 ggttagcact agctactgct ggagatagcc aggctagatt tcatctgggt aagatattct
     3901 catgcggtct tggtgtgcat caggattata agcaggctat atactggttt cagcttgcag
     3961 ctgagcaagg ccatgatgat gcccagttta gtcttggttt ggcatatcat ctggggttag
     4021 gtggatataa agatgctcaa aaagcttcgg aatggtatca gaaagctgct gagcaaggtc
     4081 atgcagaggc tcagtttcag cttggaaggc tgtatacttt ctctgattta agaaatgatg
     4141 cgttagcagt cgaatggttt ctctgtgctg cgaagcaaga ccacagtagt gcccaattta
     4201 aacttggctg gatgtaccat ctcggtatgg gcgttgagca aagtgatagg caggctttcc
     4261 attggtttat tctggccgct gagcaagatc atgcaggagc tcaggcatct cttggtgaga
     4321 tgtataaaca tggatggggg gtcgagcaag atgatgttgc tgcgcaggat tggttttatc
     4381 gtgccagaac catgcactat ccctaaaccc gccctgtgcg gggtttttta cgcctacgtg
     4441 taagaggctt gcggagctgg cttctgccga ttcataacag ggatgttatg gtaaataaca
     4501 cttaatcatt atcaacggag ttattaaagg ttgcggcgaa gccttttaat ggggtttctg
     4561 atatgtaatt agcaaacttg accatgtgtg ggtattttat tgctatgttc ctacatattg
     4621 cgtcaaatgt cggtgttgaa tactctaact cttcaacggt ttttttgacc attgaatact
     4681 tgctgggata tctcccccct cttttaataa gatatttttg aggatgattt tgtccgtgat
     4741 agttcatctg gaggcaatat ttcacggtgt agtatctaac aacgccatga ccatggttgt
     4801 atgtggatgt tattaatcca tttgagcaag agtatttttc taatttatcg taaagctctt
     4861 ttgtaataac taaagaacca atacgcccct cacgcacttc tgttattgaa aaagtcatat
     4921 ttaagctcac ttttttactc tgaatataac ctgttagaga ggattttctt gagatcatcc
     4981 gtctgtcgtc gtagtctctt atccagaaac gaaaaaacca cctggggagg tggtttttcg
     5041 aaggttcagt aagttgggga acttctgaac cgtggtaaca gggtgtacaa gaccgctgcc
     5101 accaaattcg tcc
//
