LOCUS       NZ_CP033161             6346 bp    DNA     linear   CON 26-JUN-2024
DEFINITION  Escherichia coli strain CM IVRI KOL-1 plasmid unnamed.
ACCESSION   NZ_CP033161
VERSION     NZ_CP033161.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10246265
            Assembly: GCF_011045475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6346)
  AUTHORS   Bandyopadhyay,S., Chopra,M., Bhattacharya,D., Banerjee,J.,
            Swarnkar,M., Gautam,D., Singh,A.K., Singh,R.K. and De,S.
  TITLE     Whole Genome Sequence of Pathogenic Escherichia.coli K2A
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6346)
  AUTHORS   Bandyopadhyay,S., Chopra,M., Bhattacharya,D., Banerjee,J.,
            Swarnkar,M., Gautam,D., Singh,A.K., Singh,R.K. and De,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-OCT-2018) Biotech, National Dairy Research Institute,
            Karnal, India, Model Town, Karnal, Haryana 247001, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 30-NOV-2015
            Assembly Method                   :: HGAP v. Nov-2015
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 133.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_011045475.1-RS_2024_06_26
            Annotation Date                   :: 06/26/2024 01:48:12
            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)                     :: 5,037
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,569
            CDSs (with protein)               :: 4,569
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 348
            CDSs (without protein)            :: 348
            Pseudo Genes (ambiguous residues) :: 0 of 348
            Pseudo Genes (frameshifted)       :: 178 of 348
            Pseudo Genes (incomplete)         :: 182 of 348
            Pseudo Genes (internal stop)      :: 62 of 348
            Pseudo Genes (multiple problems)  :: 66 of 348
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033161.1.
            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/
FEATURES             Location/Qualifiers
     source          1..6346
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CM IVRI KOL-1"
                     /isolation_source="Mastitis Milk"
                     /db_xref="taxon:562"
                     /plasmid="unnamed"
                     /geo_loc_name="India"
                     /lat_lon="22.5726 N 88.3639 E"
                     /collection_date="2012-10-05"
                     /collected_by="Samiran Bandyopadhyay"
     gene            complement(<1..1957)
                     /gene="mobQ"
                     /locus_tag="EAF06_RS24850"
                     /old_locus_tag="EAF06_25760"
     CDS             complement(<1..1957)
                     /gene="mobQ"
                     /locus_tag="EAF06_RS24850"
                     /old_locus_tag="EAF06_25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_164529495.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSH"
                     /name="mobQ"
     gene            2136..2390
                     /gene="mobC"
                     /locus_tag="EAF06_RS24855"
                     /old_locus_tag="EAF06_25765"
     CDS             2136..2390
                     /gene="mobC"
                     /locus_tag="EAF06_RS24855"
                     /old_locus_tag="EAF06_25765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2923..3624
                     /locus_tag="EAF06_RS24860"
                     /old_locus_tag="EAF06_25775"
     CDS             2923..3624
                     /locus_tag="EAF06_RS24860"
                     /old_locus_tag="EAF06_25775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3880..6038)
                     /gene="mobQ"
                     /locus_tag="EAF06_RS25650"
                     /old_locus_tag="EAF06_25780"
                     /pseudo=""
     CDS             complement(3880..6038)
                     /gene="mobQ"
                     /locus_tag="EAF06_RS25650"
                     /old_locus_tag="EAF06_25780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /name="mobQ"
     gene            6217..>6346
                     /gene="mobC"
                     /locus_tag="EAF06_RS25655"
                     /old_locus_tag="EAF06_25785"
                     /pseudo=""
     CDS             6217..>6346
                     /gene="mobC"
                     /locus_tag="EAF06_RS25655"
                     /old_locus_tag="EAF06_25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /name="mobC"
     Typing          complement(1600..1958)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1959..2135
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          complement(5681..6039)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          6040..6216
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2924..3624
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..2044)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.853"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3884..4620)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.09e-161"
     Typing          complement(4618..6125)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.801"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtggctgtc tgcatcgtga tttacggcaa caccataccc tgcataccgt aaccccttat
       61 cggtcagtgc actgatgacc agctggctgt tatcggctga gggaacggca aacgcgggat
      121 acagcgtacc attaagccgg acaacaccgc ccagagagtc atccacgccc atgaccagca
      181 aaagctgaag ctggcgggtt tcccggtcga cagaactcat taccggcatc agcgtcggta
      241 gcagacgtcc ctgcgtaaaa tccaccttcc ttgctgccag tgatggcatg gctggctggc
      301 ggtcttctcc aagacagaaa gactccggcc atgtcttcgg ctggcggaga ttgcgggtat
      361 attgcggcca tgtctggcaa acctgcgtca gaagttgctc aaaggtcgca gaggaataaa
      421 cacgttgcag tggtggatgt tgaccgattt cgcttcggtc acagatataa ccactcctgt
      481 cacgcattaa atcaacacgc tcaaagattc tggtgcggta tttctccagc tcgttccccc
      541 agagcgtgta ttctccgttc cggttgtgaa gcagaaggta acaggtcatt tccccgttac
      601 caggcatggg ggcctcgcca taccccgtaa cgactgcgct cagtacccct gaatccataa
      661 cggcattgtc atttttcctg agctgttccg ctcgtcgctc cgcgcgacta cgttctgtat
      721 cctcctgctc cttccggcgc aattcctctt cacgtttaag caactggact ctgagagctg
      781 caaggccgga tgccccccac tgctgccact gtttttcaaa tgccgtctga ctcgcgggaa
      841 tgtcctgttt ctccaccttc cggtaatgct gtcgcaattt ttccatttgc tggctcagcg
      901 actggatttt tccctgttcg ctacggtatt ccggtgccgc ccattgcatc aggggaatac
      961 gggaaaaacc ggacgaaaac ggcgatgatt ttttcaggct ggcagcatgg ctcatcgctt
     1021 cctttcgttc ggtgttcagc tcttcccagc gtctgcgcgt cgcctgcata tctgccatca
     1081 tcgacatggc attactggtg agtttccatg ccgcattact gtccttcggc aacgcttcga
     1141 tgatgtcacg tagtgtgtac gaagttgcgt tgtcaggaag cacgatattc agaaggtcag
     1201 ccacacggcg ggcaggctct gtcagcccgc tgtttctgag ttcggtacgg gaaatctgta
     1261 tttccaggtt aagtctgtta atcagacgat tctgttcgcc gcgttctgtt tcgataccgc
     1321 gtgtttccat cgcacaggca gactttccga ggtgaatacc aggcgttttc tcaagcccct
     1381 gtcgctcgta tgaacgatgg tctatctctt cctgataacc ggcgttcgcc agtgccctgt
     1441 tcgcatggtc agcccatgat gcacgccacg tctcggcatg tgtccggtcg ttccagtccc
     1501 tgacctttcc accgaatcca gcaggtccga cagctctcgt ggtcagcatg atgtgcgcat
     1561 ggggatttgt tttatccatg tgatggaacg ccacatcagc aatcatgccc tgactgacaa
     1621 agttttctct gacaaaggcg agaacggttt cccgtgcggc atcctgcggt agttcgcggg
     1681 ggatggcgag ttcaatttcc cgcgcaagtt gtgagttctt ccggcgttcg gccttctcaa
     1741 cggcattcca gagttcggca cggttcgtac accaggcagg ggctgtcgcg ggagtcagaa
     1801 tcacagcttc agccacaccg cttttgcggg tgtagtcgtg agtcagtccg gtacgctcat
     1861 caagcatcag tgaaccggaa cgataggcag cagaagcaac ggcgctgtag ccgctgtttc
     1921 tggagatgat tttcatgctg agatgataaa tcgccatttc tgccgtaatg cctttttgtg
     1981 gttttctttc agccccgcag ggcgcacaca atcgaaacgg agtggagatt gtataagtgc
     2041 gcacttcgtg attttccgtg cattatgcca gctcagtttt taaactacca gtgacgcgct
     2101 aaaatgcgat ttttcatcgc gcacggagtt acatcatgag cagaacactc gaacagaaga
     2161 ttgctgatgc tgaggccaga ttacagcgcc tgaaggcgaa gagcaggagt ctggacacag
     2221 cgcagaaggt cattgtgggt gcagcattgc tggcaaaggt cagaaagccg gaggaggtgc
     2281 agttgcgtgc ctggttactc cagttcctga aggcagaggt gacacgacag gctgatgtga
     2341 cgcgcatact gccgctgatt aacgagctgg aagcgctgcc aggacagtga ttgtatcgtc
     2401 cgctcgccgc agtcccagcg accgagcgtt agcgagcgag tgggcgagga agcggaagtg
     2461 aatccgtcgc ctgattgagc acatacgcac ggtttttcgg gaggtgatat gcgctgaacc
     2521 cgcatgaata ctggatttcc acagggttgg agggggtgta ttcggaactt gcaattctgc
     2581 tttcttgcaa cgcattgttt ttattggttt tttgttttca gcactccaag ttatccacag
     2641 gctcgtcgtt aagtttttag atcttgtttt taagatcttg tttttaatac ttgttttagc
     2701 gccaaaattc cttatagaaa acaaaatgtt acaatgctat aggtaatgtg atttaaggta
     2761 aaggtaatat gatttaaggt gtttaggtgg gggaatttaa ggtaaaggca atatgattta
     2821 aggtaatatt cacagaaaaa gggatattaa aataaaaagg cattgccttt cgttgagggt
     2881 atgtttatct tttattcatt accttttggg gagggatgct ctatgtcgga tctaattgcc
     2941 tataaatcca atgcgctggt tgaagccagt tataaattga ccctacagga acagcgattt
     3001 ttgttacttt gcatcggtcg attgaagtct ggggctgatg cagaatctcc aaaattgcaa
     3061 aagacaatga ccattacagc tgcggaatat ttcgattcat tccctgacat ggggcggaaa
     3121 aatgccgagg ttcagttaca ggaagcaatt gatcgtttgt gggacaggtc aatcattctc
     3181 aaggatgacg agaaacgtga ggagttccgc tggatccagt atcgggcaca gtacgctaaa
     3241 ggcgaggcca gagcacaaat aacattttct gacgcagtaa tgccttattt gacacaacta
     3301 caagggcaat ttactagagt tgtaatcaag aatatatcta gattatcaag aagttacagt
     3361 ataaggatat acgaactcct ccagcagttc cgcagtactg gcgaacgtat tatcgctctc
     3421 gatgactttc gctcaatgct tgatatagag cataaatatc aaacatataa atcacttaac
     3481 cagcaattat taagaccctg cattgacgaa ctgaacaaaa aaagcgacct ggctgtaacg
     3541 gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt caaggaagac
     3601 aaacaaatca agatgacgat ctaaaatcga ttttaaggca cctaaaacgc tccctgctgc
     3661 gttttttttg tgttagtagt gcgaaggtac tattgaagtg aaaaattgcg tcaaaagcac
     3721 tctaatgcag cgaaaaaaga acccccattt tttgggggcg gaaaaacaaa actatgcttg
     3781 cattatgtgt gtgcttcttg cattcatccc tgtcgatgaa catcgaagaa catcgacgaa
     3841 cataacacga tgttaaacaa aacaaaatat tgttcacatt cactgtgacc aaccgcgatc
     3901 atgtctcctc tcggtggcgt gtgttcgtgc atcttcctcg cgccgccatt cgtcccaggt
     3961 acgattaaaa cccagcgagc ggaacagatg atccggctgt ttttctggtg tgttgacggc
     4021 agcaaaaagc ggtgcctcac gggttttcag atgaaactcc ataagttccg gcgcaggtga
     4081 tatgtggctg tctgcatcgt gatttacggc aacaccatac cctgcatacc gtaacccctt
     4141 atcggtcagt gcactgatga ccagctggct gttatcggct gagggaacgg caaacgcggg
     4201 atacagcgta ccattaagcc ggacaacacc gcccagagag tcatccacgc ccatgaccag
     4261 caaaagctga agctggcggg tttcccggtc gacagaactc attaccggca tcagcgtcgg
     4321 tagcagacgt ccctgcgtaa aatccacctt ccttgctgcc agtgatggca tggctggctg
     4381 gcggtcttct ccaagacaga aagactccgg ccatgtcttc ggctggcgga gattgcgggt
     4441 atattgcggc catgtctggc aaacctgcgt cagaagttgc tcaaaggtcg cagaggaata
     4501 aacacgttgc agtggtggat gttgaccgat ttcgcttcgg tcacagatat aaccactcct
     4561 gtcacgcatt aaatcaacac gctcaaagat tctggtgcgg tatttctcca gctcgttccc
     4621 cagagcgtgt attctccgtt ccggttgtga agcagaaggt aacaggtcat ttccccgtta
     4681 ccaggcatgg gggcctcgcc ataccccgta acgactgcgc tcagtacccc tgaatccata
     4741 acggcattgt catttttcct gagctgttcc gctcgtcgct ccgcgcgact acgttctgta
     4801 tcctcctgct ccttccggcg caattcctct tcacgtttaa gcaactggac tctgagagct
     4861 gcaaggccgg atgcccccca ctgctgccac tgtttttcaa atgccgtctg actcgcggga
     4921 atgtcctgtt tctccacctt ccggtaatgc tgtcgcaatt tttccatttg ctggctcagc
     4981 gactggattt ttccctgttc gctacggtat tccggtgccg cccattgcat caggggaata
     5041 cgggaaaaac cggacgaaaa cggcgatgat tttttcaggc tggcagcatg gctcatcgct
     5101 tcctttcgtt cggtgttcag ctcttcccag cgtctgcgcg tcgcctgcat atctgccatc
     5161 atcgacatgg cattactggt gagtttccat gccgcattac tgtccttcgg caacgcttcg
     5221 atgatgtcac gtagtgtgta cgaagttgcg ttgtcaggaa gcacgatatt cagaaggtca
     5281 gccacacggc gggcaggctc tgtcagcccg ctgtttctga gttcggtacg ggaaatctgt
     5341 atttccaggt taagtctgtt aatcagacga ttctgttcgc cgcgttctgt ttcgataccg
     5401 cgtgtttcca tcgcacaggc agactttccg aggtgaatac caggcgtttt ctcaagcccc
     5461 tgtcgctcgt atgaacgatg gtctatctct tcctgataac cggcgttcgc cagtgccctg
     5521 ttcgcatggt cagcccatga tgcacgccac gtctcggcat gtgtccggtc gttccagtcc
     5581 ctgacctttc caccgaatcc agcaggtccg acagctctcg tggtcagcat gatgtgcgca
     5641 tggggatttg ttttatccat gtgatggaac gccacatcag caatcatgcc ctgactgaca
     5701 aagttttctc tgacaaaggc gagaacggtt tcccgtgcgg catcctgcgg tagttcgcgg
     5761 gggatggcga gttcaatttc ccgcgcaagt tgtgagttct tccggcgttc ggccttctca
     5821 acggcattcc agagttcggc acggttcgta caccaggcag gggctgtcgc gggagtcaga
     5881 atcacagctt cagccacacc gcttttgcgg gtgtagtcgt gagtcagtcc ggtacgctca
     5941 tcaagcatca gtgaaccgga acgataggca gcagaagcaa cggcgctgta gccgctgttt
     6001 ctggagatga ttttcatgct gagatgataa atcgccattt ctgccgtaat gcctttttgt
     6061 ggttttcttt cagccccgca gggcgcacac aatcgaaacg gagtggagat tgtataagtg
     6121 cgcacttcgt gattttccgt gcattatgcc agctcagttt ttaaactacc agtgacgcgc
     6181 taaaatgcga tttttcatcg cgcacggagt tacatcatga gcagaacact cgaacagaag
     6241 attgctgatg ctgaggccag attacagcgc ctgaaggcga agagcaggag tctggacaca
     6301 gcgcagaagg tcattgtggg tgcagcattg ctggcaaagg tcagaa
//
