LOCUS       NC_020517               4621 bp    DNA     linear   CON 27-OCT-2020
DEFINITION  Bifidobacterium breve UCC2003, complete sequence.
ACCESSION   NC_020517
VERSION     NC_020517.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02604112
            Assembly: GCF_000220135.1
KEYWORDS    RefSeq.
SOURCE      Bifidobacterium breve UCC2003
  ORGANISM  Bifidobacterium breve UCC2003
            Bacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae;
            Bifidobacterium.
REFERENCE   1  (bases 1 to 4621)
  AUTHORS   O'Connell Motherway,M., Zomer,A., Leahy,S.C., Reunanen,J.,
            Bottacini,F., Claesson,M.J., O'Brien,F., Flynn,K., Casey,P.G.,
            Munoz,J.A., Kearney,B., Houston,A.M., O'Mahony,C., Higgins,D.G.,
            Shanahan,F., Palva,A., de Vos,W.M., Fitzgerald,G.F., Ventura,M.,
            O'Toole,P.W. and van Sinderen,D.
  TITLE     Functional genome analysis of Bifidobacterium breve UCC2003 reveals
            type IVb tight adherence (Tad) pili as an essential and conserved
            host-colonization factor
  JOURNAL   Proc Natl Acad Sci U S A 108 (27), 11217-11222 (2011)
   PUBMED   21690406
REFERENCE   2  (bases 1 to 4621)
  AUTHORS   O'Connell Motherway,M., Zomer,A., Leahy,S., Reunanen,J.,
            Bottacini,F., Claesson,M., O'Brien,F., O'Flynn,K., Casey,P.,
            Moreno-Munoz,J., Higgins,D.G., Shanahan,F., de Vos,W.,
            Fitzgerald,G.F., Ventura,M., O'Toole,P. and van Sinderen,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAR-2006) Department of Microbiology, Alimentary
            Pharmabiotic Centre, University College Cork, College Road, Cork,
            Munster, Ireland
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/25/2020 15:03:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.13
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 2,069
            CDSs (total)                      :: 2,006
            Genes (coding)                    :: 1,904
            CDSs (with protein)               :: 1,904
            Genes (RNA)                       :: 63
            rRNAs                             :: 2, 2, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 2, 2 (5S, 16S, 23S)
            tRNAs                             :: 54
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 53 of 102
            Pseudo Genes (incomplete)         :: 60 of 102
            Pseudo Genes (internal stop)      :: 16 of 102
            Pseudo Genes (multiple problems)  :: 24 of 102
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP000303.1.
            Source DNA or strain is available from Douwe van Sinderen,
            d.vansinderen@ucc.ie.
            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..4621
                     /organism="Bifidobacterium breve UCC2003"
                     /mol_type="genomic DNA"
                     /strain="UCC2003"
                     /db_xref="taxon:326426"
     gene            complement(1..1119)
                     /locus_tag="BBR_RS11735"
                     /old_locus_tag="Bbr_0283"
     CDS             complement(1..1119)
                     /locus_tag="BBR_RS11735"
                     /old_locus_tag="Bbr_0283"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015438347.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955"
                     /protein_id="WP_015438347.1"
                     /translation="MSERTTSAVADKPTPTMRDVAQLAGVSVTSVSNYLSDYPYMKQTT
                     RERIRQAIEMLGYVTDERARSLRSGRTGLISLAIPSLTQIYFAELAERVIAAARRRGYG
                     VTVESTAFSRRHELESVAAMARKMSDGLILSPLLMERRDIARLAGDYPLVVLGECLFDV
                     SAPHILVHNIDAVKALTQHLLDAGCRRIALIGGALDRRRTSTETLRTQGYLEALAQAGV
                     PVDAKLIRPIPAWETDEEAKDDASGGAGYVGRGIATRRNGSEIVRRMFEEGIKADALLC
                     YNDLLAFGALRQLREMGVRIPDDLRVVSMDNLEEAQYTIPSLTSVELGKEQIAQCAVDA
                     ILEQVAGGGRGAAEQRYVDFSIHYRESSPAVA"
     gene            complement(1282..2727)
                     /locus_tag="BBR_RS11740"
                     /old_locus_tag="Bbr_0284"
     CDS             complement(1282..2727)
                     /locus_tag="BBR_RS11740"
                     /old_locus_tag="Bbr_0284"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012576706.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|A7ZUZ0|2.A.2.1.1"
                     /protein_id="WP_015438348.1"
                     /translation="MTSATAAAPVKSSNADKVSLKEYVAYFCYGFGQCFSYGIIGSFIL
                     IYYTDVVGISSVVASAIFLVARLWDAVFDPLVSGFMDSRKPSKQGKFRKWMKIAPIFVV
                     VATIACFIDPDIPVAGKIVFCGATYILWGTCYAFSDIPFWSLSTVMSHDRQTRTDLVTV
                     ANIGVSAGIAMAGIIMPVMLAQFKQNNTPSMSYLISVSILMIAGFVIMEFGYLFTKERI
                     AASDKAEKLSYKQVFEAVKANKYMMMILVIFFLKFFMEMVNNMMIYFFTYNMSNAGLMS
                     GFGLIGTFSALTFLLIPVLTRRYKKVNLVRVLLIAEIAFRVVFYFVGYSNTTLTFVFIG
                     ITWCMYSMSNPILSAMLAETIEYSQVKTGHRAEAVVFGGQTFSSKLAIALAGATTGLTL
                     TFLGYQPNVAQTSGTLNGLFIVISILPALGALLKLLILTKYDYTETEFKECQRILVERG
                     AEGYQTAPADLVSETAASGSATK"
     gene            complement(2801..4621)
                     /locus_tag="BBR_RS11745"
                     /old_locus_tag="Bbr_0285"
     CDS             complement(2801..4621)
                     /locus_tag="BBR_RS11745"
                     /old_locus_tag="Bbr_0285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012576707.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="3.2.1.23|GH2"
                     /protein_id="WP_012576707.1"
                     /translation="MERIQYPDPQCVRRNWVDLNGTWDFAIPGAPAGTKNGNQGNNAME
                     STPETLQAAASMAFPEFDRTIEVPYSYTFPKSGVDEPQYHPVVWYRRSFDLDMRPGKRY
                     LLNFEAVDYACDVWLNGRHVGSHQGGHTPFRFDVTPYAAKENELVVKVVDFNRTDQPLG
                     KQAWKDGNFACWYTRTIGIWQSVWLEETGDVHLTDFTMTPHANQARLDVDASLNVNVDA
                     ELDYNVTFEGKPVTHGTVSFTNARARFSVEIRNYDPSPEPHPWTPSTPDLYDIDFTVRS
                     GGETTDEVSSYFGLRDVTSDGKMIFLNDQKYYMKLLLNQGYYPGGGLTGTADEFRADIE
                     KMKAMGFNGNRIHQKLESNRMLYLCDKLGFIVWAEMPSAYEFGPELIANVERELPAYLR
                     KHVNHPSVFAYVLMNESWGVFDIAHSEQERTFVNSLYYQAKAFDPSRLVIGNDGYEQTR
                     TDIATIHDYNADADELLETYQGRRDEVLAGAPSPMGGRRVFCQGYEQQRVPVMVTEYGG
                     VAYEPGGHTEDSWGYGERITDPDKVVDQIAALTRAVMDIDYCVGFCYTQTSDVEQEVNG
                     LLDHDHEYKFDPKRIREVLLSKHTYGYVQV"
ORIGIN
        1 tcacgccacc gccggcgagc tctcccggta gtggatcgag aaatcgacgt aacgctgctc
       61 ggctgcgccg cgcccgccgc cggccacttg ctccagaatg gcgtcgaccg cgcattgcgc
      121 gatctgctcc ttgccaagct cgacggaggt cagcgaggga atcgtgtatt gcgcctcctc
      181 gaggttgtcc atgctgacca cgcgcaggtc gtccgggatg cgcacgccca tctcgcgcag
      241 ttgtcgcaac gcaccgaagg cgagcaggtc gttgtagcac agaagggcgt cggccttgat
      301 gccttcctcg aacatgcgac gcacgatttc cgaaccgttg cgtctggtgg cgatgccccg
      361 tcccacatag cctgcgccgc cgctggcatc gtccttggcc tcctcgtcgg tctcccaggc
      421 ggggatgggc ctgatgagct tggcatccac tggcacgccg gcctgtgcca atgcttcgag
      481 atatccctgc gtacgcagcg tttcggttga ggtccgtcgt cggtcgagcg cgccgccgat
      541 cagcgcgatg cgccggcaac ccgcgtcgag cagatgctgg gtcagcgcct tgaccgcgtc
      601 gatgttatgc acgaggatat ggggcgcgga cacgtcaaac aggcactcgc cgagcacgac
      661 gagcggatag tcgccggcca ggcgggcgat gtcgcggcgt tccatgagca gggggctcag
      721 aatcaacccg tcactcatct tgcgcgccat ggcggcgacg ctttccaact catgtcgccg
      781 actgaaggcc gtagattcca cggttacgcc gtatccgcgt cgccgtgccg cggcaatcac
      841 gcgttcggcg agctcggcga aatatatctg ggtgagactg ggaatggcca gggatatcag
      901 cccggttctc cccgagcgca ggctgcgtgc ccgttcgtcg gttacatatc ccagcatctc
      961 gatggcctgc cggatgcgtt cgcgggtagt ctgcttcata tacgggtaat cggaaagata
     1021 gttggacacc gaggtcaccg acaccccggc gagctgcgcg acgtcgcgca tggtgggggt
     1081 gggtttgtcg gcgacggccg atgtcgttct ttcactcaca ggtggctctt ttctcgggtg
     1141 ggcgcccacc gtccggcggt gcgtttcctc ccatcataac gacggccgtc ccgttctccc
     1201 gaaacgtcga agggctccgt gtccgatgcc ggaacgcatc ggacacggag ccctctcagt
     1261 cattgtgtgg agcggatatc cttactttgt cgccgagcca gacgcggcgg tctcggacac
     1321 cagatcggcg ggtgcggtct ggtatccctc cgcgccgcgt tcgaccagga tgcgctggca
     1381 ttccttgaac tcggtctcgg tgtagtcgta cttcgtcaga atcagcagct tgagcagcgc
     1441 gcccagcgcc ggcaggatcg agatcacgat gaacaggccg ttcagcgtgc ccgacgtctg
     1501 cgcgacgttc ggctgatagc cgaggaaagt gagcgtcaga ccggtcgtgg cgccggcgag
     1561 ggcgatggcc agcttgctgg agaaggtctg gccgccgaag accacggcct ccgcacggtg
     1621 cccggtcttg acctggctgt attcgatggt ctcggccagc atggcggaca ggatcgggtt
     1681 gctcatcgag tacatgcacc aggtgatgcc gatgaacacg aaggtcaatg tcgtgttcga
     1741 gtatccgacg aagtagaaga ccacgcggaa ggcgatctcg gcgatgagca gcacgcggac
     1801 gaggttcacc ttcttgtagc ggcgggtcag caccgggatg agcaggaagg tcagcgcgct
     1861 gaaggtgccg atcaggccga agccactcat cagcccggcg ttcgacatgt tgtaggtgaa
     1921 gaagtagatc atcatgttgt tgaccatttc catgaagaac ttcaggaaga agatcaccag
     1981 gatcatcatc atgtacttgt tcgccttgac ggcctcgaac acctgcttgt aggagagctt
     2041 ctccgccttg tcggaggcgg cgatgcgctc cttggtgaac aggtagccga actccatgat
     2101 cacgaagccc gcgatcatga ggatcgacac ggagatcaga tagctcatcg acggagtgtt
     2161 gttctgcttg aactgcgcga gcatcaccgg catgatgatg ccggccatgg cgatgccggc
     2221 ggacacgccg atgttggcga cggtcactag gtcggtgcgg gtctggcggt catgcgacat
     2281 cacggtggac agcgaccaga acgggatgtc ggagaaggcg tagcaggtgc cccacaggat
     2341 gtaggtggcg ccgcagaaga cgatcttgcc ggccaccggg atgtccgggt cgatgaagca
     2401 ggcgatcgtc gcgacgacca cgaagatcgg ggcgatcttc atccacttgc ggaacttgcc
     2461 ttgcttgctg ggcttgcggg agtccatgaa cccggagacc agcgggtcga agacggcgtc
     2521 ccacaggcgg gcgaccagga agatcgcgct ggcgaccacc gaggagatgc cgaccacatc
     2581 cgtgtagtag atcaggatga agctgccgat gatgccgtag ctgaagcact gtccgaatcc
     2641 gtagcagaaa tacgccacgt attccttgag gctcactttg tccgcattgc tggatttgac
     2701 cggtgcggct gccgttgccg atgtcatatt gttccctttc tctatttatt ggttcgattg
     2761 tgaagggtgg ccatatccgc acccatgtcg gcgctcgttc tcacacctgc acgtagccgt
     2821 aggtgtgctt gctcagcagc acctctcgta tgcgcttggg gtcgaatttg tattcgtggt
     2881 cgtggtcgag caggccgttg acctcctgtt ccacgtcgga ggtctgcgtg tagcagaagc
     2941 caacgcaata gtcgatgtcc atcacggccc gcgtcagggc cgcgatctga tcaacgacct
     3001 tgtcggggtc ggtgatacgc tcaccgtagc cccacgaatc ctcggtgtga ccgcccggct
     3061 cataggccac gccgccgtat tcggtgacca tcaccggcac gcgctgctgt tcgtacccct
     3121 ggcagaacac gcggcggccg cccatcgggg agggtgctcc agccaacact tcgtcgcgac
     3181 ggccctgata ggtctccagc agttcgtcgg catcggcgtt gtagtcgtgg atcgtggcga
     3241 tgtcggtgcg cgtctgctcg tagccatcgt tgccgatgac caggcgcgag ggatcgaagg
     3301 ccttcgcctg ataatagagc gagttgacga aggtgcgctc ctgctcgctg tgggcgatgt
     3361 cgaagacgcc ccacgactcg ttcatcagca cataggcgaa caccgagggg tggttgacgt
     3421 gcttgcgcag gtaggcgggc agctcgcgct ccacattggc gatgagctcc gggccgaatt
     3481 cgtaggcgct gggcatctcg gcccagacga tgaaaccgag cttgtcgcac aggtagagca
     3541 tgcggttgga ctcgagcttc tgatggatgc ggttgccgtt gaagcccatg gccttcatct
     3601 tctcgatgtc ggcgcggaac tcgtcggcgg tgcccgtcaa tcctccgccc gggtaatagc
     3661 cctggttgag cagcagcttc atgtagtact tctggtcgtt gaggaagatc atcttcccgt
     3721 cgctggttac atcacgcaga ccgaagtagc tggacacctc gtcggtggtc tcgccgccgg
     3781 agcgcacggt gaagtcgatg tcgtagaggt ccggcgtcga gggcgtccat ggatgcggtt
     3841 cgggggacgg gtcgtagttg cggatctcga cggagaaccg ggcgcgcgcg ttggtgaagg
     3901 agacggtgcc gtgcgtgacc ggcttgcctt cgaaggtcac gttgtagtcg agctccgcgt
     3961 cgacgttgac attgagcgag gcatccacgt cgaggcgcgc ttggttggcg tgcggggtca
     4021 tcgtgaagtc ggtcagatgc acgtcgccgg tctcttcgag ccacacgctc tgccagatgc
     4081 cgatggtgcg cgtgtaccag caggcgaagt tgccgtcctt ccatgcctgc ttgccgagcg
     4141 gttggtcggt gcggttgaaa tcgacgacct tgacgaccag ttcgttttcc ttggccgcgt
     4201 aaggcgtcac atcgaagcgg aagggcgtgt gtccgccttg gtgcgagccg acatgtcggc
     4261 cgttgagcca cacgtcgcag gcatagtcga cggcctcgaa gttgagcagg tatcgtttgc
     4321 ccgggcgcat gtcgaggtcg aaggagcggc ggtaccacac gacggggtga tactgcggtt
     4381 cgtccacgcc ggacttgggg aaggtgtagc tgtagggcac ctcgatggtg cggtcgaatt
     4441 cggggaaggc catcgaggcc gcggcttgga gggtctcggg tgtggactcc atcgcgttgt
     4501 tgccttggtt gccgttcttg gtcccggccg gtgcgccggg gatcgcgaag tcccaggtgc
     4561 cgttgagatc gacccagttg cgtcggacgc attgggggtc ggggtattgg attcgctcca
     4621 t
//
