LOCUS       MSTC01000063            4634 bp    DNA     linear   BCT 01-FEB-2017
DEFINITION  Lactobacillus rhamnosus strain AMC010 contig_37, whole genome
            shotgun sequence.
ACCESSION   MSTC01000063
VERSION     MSTC01000063.1
DBLINK      BioProject: PRJNA357881
            BioSample: SAMN06161582
KEYWORDS    WGS.
SOURCE      Lactobacillus rhamnosus
  ORGANISM  Lactobacillus rhamnosus
            Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
            Lactobacillus.
REFERENCE   1  (bases 1 to 4634)
  AUTHORS   Arnold,J., Altermann,E., Thompson,A. and Azcarate-Peril,M.A.
  TITLE     Genome sequencing of stool bacterial isolates from healthy human
            infants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4634)
  AUTHORS   Arnold,J., Altermann,E., Thompson,A. and Azcarate-Peril,M.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JAN-2017) Cell Biology and Physiology, University of
            North Carolina at Chapel Hill, 109 Mason Farm Road, Chapel Hill, NC
            27599, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Newbler v. 2.7; SPAdes v. 3.8
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 30.0x
            Sequencing Technology             :: 454; IonTorrent
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 01/04/2017 12:39:01
            Annotation Pipeline               :: NCBI Prokaryotic Genome
            Annotation Method                 :: Best-placed reference protein
            Annotation Software revision      :: 4.0
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
            Genes (total)                     :: 3,230
            CDS (total)                       :: 3,171
            Genes (coding)                    :: 2,715
            CDS (coding)                      :: 2,715
            Genes (RNA)                       :: 59
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 53
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 456
            Pseudo Genes (ambiguous residues) :: 3 of 456
            Pseudo Genes (frameshifted)       :: 384 of 456
            Pseudo Genes (incomplete)         :: 49 of 456
            Pseudo Genes (internal stop)      :: 44 of 456
            Pseudo Genes (multiple problems)  :: 22 of 456
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from M. Andrea Azcarate-Peril,
            University of North Carolina at Chapel Hill.
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            Annotation Pipeline
            set; GeneMarkS+
            repeat_region
            partial rRNAs                     ::
FEATURES             Location/Qualifiers
     source          1..4634
                     /organism="Lactobacillus rhamnosus"
                     /mol_type="genomic DNA"
                     /submitter_seqid="contig_37"
                     /strain="AMC010"
                     /isolation_source="infant stools"
                     /host="Homo sapiens"
                     /db_xref="taxon:47715"
                     /country="USA"
                     /collection_date="2011"
     gene            1..1794
                     /locus_tag="BVG98_10115"
     CDS             1..1794
                     /locus_tag="BVG98_10115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005714409.1"
                     /note="phosphoenolpyruvate-dependent sugar
                     phosphotransferase system; catalyzes the phosphorylation of
                     incoming sugar substrates concomitant with their
                     translocation across the cell membrane; IIB is
                     phosphorylated by IIA and then transfers the phosphoryl
                     group to the sugar; IIC forms the translocation channel;
                     Derived by automated computational analysis using gene
                     prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|P11162|4.A.3.1.1"
                     /protein_id="ONF99735.1"
                     /translation="MQVIVKRLEKHQALFEKISRNIYLMAIKDGFLAAMPIILFSSIFI
                     LLSNIPPLIGIKVPVDLNAWFNKIYNYTMGFVGFYVAGTTAKALTGSMNQRIKGGRFLN
                     NTSTMMASMVGFMLLAIGTTSKGNFLPTFFGTQGILSAFVAAFVTVWVYKFCVERDLTI
                     KMPKEVPGAISQNFRDIIPFGAATLIFSLIDVASRAALKVPFSAIIATVLAPVFKGAET
                     YPGMMFIWFLIPMFWFLGVHGPSVVKPALESALFGNTTANLDLFKAGNFPYHALTENFG
                     NFVGELGGTGATFIVPFLFMFFMKSKQLKAIGKASFIPVMFAVNEPLLFGAPIILNPYF
                     LIPFVLAPVVNVVIGKAFIDFHIMRGFMYFMSWALPGPIGAFIDTNFQWTSLLLMAILL
                     TVDALIYMPFIKAYDAELLEQEAAVDAGTATAAATAGASEVTAEADAATAQEFPEPEEV
                     KQAETAKQEEANQNPAAGKKLDHELKVLVLCAGGGTSEQLANALTEGAKEYHEPIVASA
                     GAYGSHHDILPNYDLVVLAPQVRTYYSDLKHDTDRLGIKLVATKGQQYIALTRDPEKAL
                     DFIVENYKDVEKKPQDSSDSK"
     gene            1851..2718
                     /locus_tag="BVG98_10120"
                     /pseudo=""
     CDS             1851..2718
                     /locus_tag="BVG98_10120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003660216.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /protein_id="WP_003660216.1"
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
     gene            2819..3184
                     /locus_tag="BVG98_10125"
     CDS             2819..3184
                     /locus_tag="BVG98_10125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005691321.1"
                     /note="catalyzes the phosphorylation of incoming sugar
                     substrates concomitant with their translocation across the
                     cell membrane; protein IIA transfers a phosphoryl group to
                     IIB which then transfers the phosphoryl group to the sugar;
                     IIC forms the translocation channel for the sugar uptake;
                     Derived by automated computational analysis using gene
                     prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|Q045H4|4.A.3.1.3"
                     /protein_id="ONF99736.1"
                     /translation="MATKEEISMTGFAIVAYAGDAKTDLIEALNEARKGNFEHARSLVK
                     EARQSIDDAHNEQTKLLSKEAGGENMDVTFIMVHGQDTLMTTMMLLDTISFTIDEYERL
                     AAIEKQLGIALPTNDIH"
     gene            3210..4634
                     /locus_tag="BVG98_10130"
     CDS             3210..4634
                     /locus_tag="BVG98_10130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005691323.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GH1"
                     /protein_id="ONF99737.1"
                     /translation="MTSLLNRVQSLPKGFVWGGATAAYQVEGATKVDSKGKTMWDDYLK
                     AQGRFSPDPASDFYHLYPEDIELAKLYGLNAIRVSIAWTRIFPDGYGEPNQAGVAYYHR
                     LFKCCLDNGITPYVSLHHFDSPKTLFDDGDWLNRKNIDYFVDYVDFCFKEFPEVKNWFT
                     INELISLAFSQYIQGNFPPNHHFDVTSAIQAQHNELLAHARVVNLFKEKGYQGRIGLIH
                     VLQPVYPYPDTPANEHAAALEDAFMNRFLLDGTFKGEYTPETMALINELLKANHAKLEI
                     EPGDMDVLKQASTQNDYFGMNYYQPSFVAAYEGESTNSFNGTGEKGTSSFKFQGVGQHV
                     KNPDVPTTDWDWNIYPAGMYDMLKRVAREYPNSKTIYITENGLGYKDKYEGIGNLIEDD
                     KRIDFIDQHVAALLKARSEGVDVQGYFVWSLQDQFSWANGYNKRYGLFYVNFETQAREI
                     KKSALWFRELGKTLKN"
ORIGIN
        1 atgcaagtca ttgttaaacg acttgagaaa catcaggcgt tgtttgaaaa aatctcgcgt
       61 aatatttacc tgatggccat taaagatggt tttctggcag caatgccgat tattctgttc
      121 tccagtattt tcattctatt atcaaatatt ccgccactga ttgggattaa ggttccagtt
      181 gatctcaacg catggttcaa taagatttat aactacacaa tgggttttgt tggtttttat
      241 gttgccggga cgacagccaa ggccttaact ggatcgatga atcaacgaat taaaggtggg
      301 cgctttctca acaatacgtc aacgatgatg gcttcaatgg taggattcat gctgttggcg
      361 attggcacca ccagtaaagg caacttctta ccaacattct ttggcacaca agggattttg
      421 tctgcctttg ttgcagcgtt tgtgactgtt tgggtctaca aattctgtgt tgaacgtgat
      481 ttgaccatca agatgcctaa agaagtgcct ggagccattt cccagaactt ccgtgatatt
      541 attccgttcg gtgctgcaac tttaattttt tcactcattg atgttgcctc acgtgcggcg
      601 ttgaaagtgc cattcagtgc tattattgcg actgtgcttg cgcctgtctt taaaggtgct
      661 gagacatatc ctggcatgat gtttatttgg ttcttaatcc cgatgttctg gttcttgggc
      721 gtacacggac catcagttgt caagccagct cttgaatcag cattgtttgg gaacaccacc
      781 gccaatttgg acttgtttaa ggccggaaac tttccatatc atgcactgac cgaaaatttt
      841 ggtaactttg ttggtgaact tggtggtacc ggggcgacct ttattgtccc gtttctattc
      901 atgtttttca tgaaatcaaa acaattaaaa gcgattggta aagcatcatt tatccccgtt
      961 atgttcgcgg tcaatgaacc actgctgttc ggtgcaccaa tcatcttgaa tccttacttc
     1021 ttaattccgt ttgttttggc cccagtcgtt aatgttgtaa ttgggaaggc gtttattgat
     1081 ttccatatca tgagaggctt tatgtacttc atgtcgtggg cattgcctgg gccgattggt
     1141 gcattcatcg ataccaattt ccagtggact tctttgctgc ttatggcaat tttgctaact
     1201 gtggatgcgc tgatctatat gccatttatt aaagcgtacg atgctgaact gcttgaacaa
     1261 gaagctgctg tcgatgccgg cactgcaacc gctgcagcaa ctgctggtgc aagtgaagtt
     1321 acagctgaag cagatgcagc aacggcacaa gaattcccag aaccggaaga ggtaaagcag
     1381 gctgaaacag ctaagcaaga ggaagctaat caaaatccag ctgcaggaaa gaaactcgat
     1441 catgagttga aagtattagt gctatgtgct ggtggtggta caagcgaaca attagccaat
     1501 gccttgactg aaggcgctaa agagtatcat gaaccaatcg ttgccagtgc aggtgcatat
     1561 ggctcacatc atgatatttt gccaaactat gatctggttg ttctggcacc acaagttcga
     1621 acctactaca gtgacttaaa gcatgatacg gatcgtttgg ggattaaact tgttgcaact
     1681 aaaggtcaac aatatatagc cttaacgcgt gatcctgaaa aggcattgga ttttattgtt
     1741 gaaaattata aggatgtcga aaagaaacca caagatagtt cagattcaaa gtaaatatgt
     1801 tgacttaatt taaaatcaag cgaaaagaaa ggtaaggcgg tgtatcgatg ttgctaaagg
     1861 tcaagcaagt ctataacaat aatgctgtac ttgtagacgt tggcaacggt aaagaggcga
     1921 ttcttcaggg gaaaggaatt ggtttcagca agcgtaaagg tgatgacgtt gatccaaaag
     1981 cgagttcgga aatactttat ctaaatgata cgcaagtcaa aaaatcactt tacatcttta
     2041 ctcaaagatg taccgattga cattgttgtt gctacatttg gtgtgatcgg aatggcaaaa
     2101 aagaagtatc actatccggt tttgaactat atttatgtca cacttacgga ccacgtcttt
     2161 cagatgtata aacgattgac tgccggcaaa tatcaagcta gtccagcgcc tgacatccgt
     2221 gatcgttacc cgttgcctta ccagatcgca gccgatgcgc gccgacagct taaccatgat
     2281 cttggcgttc agtttcctga agccgaaatt aagaatattg ccttacattt tattaatgca
     2341 aagggagtgg atggcgaact ggatccgacc gtgaccctga cggcgcgcgt caatgcaatc
     2401 gtgacacaag tatttgctaa atatgggtta aatcgcaatt ttgctaatca aaattacttc
     2461 gatcggctaa tgattcattt gcaatacctt gttgaacgtt taaataccaa tgagcaagac
     2521 gaggctgacc ttggtccgga aattggtcag gacttcaggc gcctttatcc caaatcgttt
     2581 acgatcgcaa ctgaaatttg tacggagctg gaaaaagcct tacaaattaa gctcaacgaa
     2641 aacgagcatg tgtactttat tatccatatt caacggctca tccaagaacc gcaaacactt
     2701 ccgcctgaat atccatagcc gtgggtggga gtttagaaag taatcttggc ttagagcgat
     2761 ttaggcttaa gaaatcgctg ctagcgtaga ggattttcaa accaagggag gaattttgat
     2821 ggcaaccaaa gaagagattt caatgaccgg ttttgcaatt gttgcttatg ccggtgatgc
     2881 gaaaaccgat ttaattgaag cattgaacga ggctcgtaaa ggcaacttcg aacatgcccg
     2941 ctcacttgtt aaagaagcgc gtcaaagtat cgatgacgcc cataatgaac aaaccaaact
     3001 gcttagtaaa gaggcaggcg gcgagaatat ggatgttact ttcatcatgg ttcatggcca
     3061 agatacgcta atgaccacga tgatgctgct agatacgatt agtttcacga ttgatgagta
     3121 tgaacgactg gcggcaattg aaaaacaatt aggcattgca ttgccaacaa acgatatcca
     3181 ttaaagtatc aaacgaaagg agtatcattg tgacaagttt attgaatcgc gttcaatcac
     3241 tgcctaaagg ttttgtttgg ggtggagcga ctgctgctta tcaggtagaa ggcgccacca
     3301 aggtagacag taaaggcaaa accatgtggg atgactatct gaaagctcaa ggcagatttt
     3361 cgcctgaccc agccagtgat ttttatcatc tttatccaga agatattgaa ctcgccaagc
     3421 tctatgggtt gaatgctatt cgggtttcga ttgcctggac acggatcttc ccagatggtt
     3481 acggtgaacc taatcaagct ggggtcgcat actatcatcg tttgtttaag tgctgccttg
     3541 ataacggcat taccccgtat gtttcgctgc atcacttcga ttcacctaaa acgctgttcg
     3601 atgatgggga ttggctgaac cgtaagaata tagactattt tgtcgattat gtcgattttt
     3661 gctttaaaga atttccggaa gttaagaact ggttcaccat caatgagctc atctcgttag
     3721 ccttttcgca atacattcaa ggcaacttcc cgccaaatca tcactttgat gttaccagtg
     3781 ctattcaagc gcagcacaac gaactgttag cccatgcgcg cgtggtcaac ttgtttaagg
     3841 aaaaaggcta tcaaggacga atcggattga ttcatgtgct gcagccggta tatccgtacc
     3901 cggatacacc agctaatgag catgctgcgg cacttgaaga tgccttcatg aatcggttcc
     3961 tgctggatgg tacgtttaaa ggcgaatata cgcccgaaac gatggcgttg atcaatgaat
     4021 tgctgaaggc caaccatgcc aagcttgaaa tcgaaccagg cgatatggat gtgttgaagc
     4081 aagcgtccac gcaaaatgat tactttggca tgaattacta tcaaccttct tttgttgctg
     4141 cctacgaagg tgaaagcaca aattcgttta atggtaccgg cgaaaaaggg accagttcct
     4201 ttaagttcca aggggttggc cagcacgtca aaaatccgga tgtgccgacg actgattggg
     4261 actggaatat ttatccggct ggcatgtacg acatgctcaa acgagtagct cgcgaatatc
     4321 caaatagcaa gacgatttac attactgaaa atggccttgg ttataaggat aagtatgaag
     4381 gcattggcaa cctcattgaa gatgacaaac gcatcgattt tattgatcaa catgttgctg
     4441 cgttactaaa agcccgcagt gaaggcgttg atgtccaagg ttacttcgtt tggtcgctgc
     4501 aggatcaatt ttcatgggcc aatgggtata acaaacgata tgggttattc tatgtcaact
     4561 ttgaaaccca agcgcgcgaa attaagaaga gcgcactgtg gtttagagaa ttaggtaaaa
     4621 ccttaaaaaa ttaa
//
