LOCUS       MSTB01000008            4631 bp    DNA     linear   BCT 01-FEB-2017
DEFINITION  Lactobacillus rhamnosus strain AMC143 contig_35, whole genome
            shotgun sequence.
ACCESSION   MSTB01000008
VERSION     MSTB01000008.1
DBLINK      BioProject: PRJNA357881
            BioSample: SAMN06161581
KEYWORDS    WGS.
SOURCE      Lactobacillus rhamnosus
  ORGANISM  Lactobacillus rhamnosus
            Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
            Lactobacillus.
REFERENCE   1  (bases 1 to 4631)
  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  JOURNAL   Unpublished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 4631)
  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 09:32:37
            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)                     :: 2,887
            CDS (total)                       :: 2,835
            Genes (coding)                    :: 2,094
            CDS (coding)                      :: 2,094
            Genes (RNA)                       :: 52
            rRNAs                             :: 1, 1 (16S, 23S)
            complete rRNAs                    :: 1, 1 (16S, 23S)
            tRNAs                             :: 47
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 741
            Pseudo Genes (ambiguous residues) :: 6 of 741
            Pseudo Genes (frameshifted)       :: 687 of 741
            Pseudo Genes (incomplete)         :: 46 of 741
            Pseudo Genes (internal stop)      :: 27 of 741
            Pseudo Genes (multiple problems)  :: 24 of 741
            CRISPR Arrays                     :: 2
            ##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..4631
                     /organism="Lactobacillus rhamnosus"
                     /mol_type="genomic DNA"
                     /submitter_seqid="contig_35"
                     /strain="AMC143"
                     /isolation_source="infant stools"
                     /host="Homo sapiens"
                     /db_xref="taxon:47715"
                     /country="USA"
                     /collection_date="2010"
     gene            1..1793
                     /locus_tag="BT102_01370"
                     /pseudo=""
     CDS             1..1793
                     /locus_tag="BT102_01370"
                     /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;
                     frameshifted; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /protein_id="WP_005714409.1"
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|P11162|4.A.3.1.1"
                     /translation="MQVIVKRLEKHQALFEKISRNIYLMAIKDGFLAAMPIILFSSI
                     FILLSNIPPLIGIKVPVDLNAWFNKIYNYTMGFVGFYVAGTTAKALTGSMNQRIKGG
                     RFLNNTSTMMASMVGFMLLAIGTTSKGNFLPTFFGTQGILSAFVAAFVTVWVYKFCV
                     ERDLTIKMPKEVPGAISQNFRDIIPFGAATLIFSLIDVASRAALKVPFSDIIATVLA
                     PVFKGAETYPGMMFIWFLIPMFWFLGVHGPSVVKPALESALFGNTTANLDLFKAGNF
                     PYHALTENFGNFVGELGGTGATFIVPFLFMFFMKSKQLKAIGKASFIPVMFAVNEPL
                     LFGAPIILNPYFLIPFVLAPVVNVVIGKAFIDFHIMRGFMYFMSWALPGPIGAFIDT
                     NFQWTSLLLMAILLTVDALIYMPFIKAYDAELLEQEAAVDAGTATAAATAGASEVTA
                     EADAATAQEFPEPEEVKQAETAKQEEANQNPAAGKKLDHELKVLVLCAGGGTSEQLA
                     NALTEGAKEYHEPIVASAGAYGSHHDILPNYDLVVLAPQVRTYYSDLKHDTDRLGIK
                     LVATKGQQYIALTRDPEKALDFIVENYKDVEKKPQDSSDSK"
     gene            1847..2716
                     /locus_tag="BT102_01375"
     CDS             1847..2716
                     /locus_tag="BT102_01375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005691319.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="ONG01734.1"
                     /translation="MLLKVKQVYNNNAVLVDVGNGKEAILQGKGIGFSKRKGDDVDPKA
                     SSEILYLNDTQVKNHFTSLLKDVPIDIVVATFGVIGMAKKKYHYPVLNYIYVTLTDHVF
                     QMYKRLTAGKYQASPAPDIRDRYPLPYQIATDARRQLNHDLGVQFPEAEIKNIALHFIN
                     AKGVDGELDPTVTLTARVNAIVTQVFAKYGLNRNFANQNYFDRLMIHLQYLVERLNTNE
                     QDEADLGPEIGQDFRRLYPKSFTIATEICTELEKALQIKLNENEHVYFIIHIQRLIQEP
                     QTLPPEYP"
     gene            2817..3182
                     /locus_tag="BT102_01380"
     CDS             2817..3182
                     /locus_tag="BT102_01380"
                     /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="ONG01735.1"
                     /translation="MATKEEISMTGFAIVAYAGDAKTDLIEALNEARKGNFEHARSLVK
                     EARQSIDDAHNEQTKLLSKEAGGENMDVTFIMVHGQDTLMTTMMLLDTISFTIDEYERL
                     AAIEKQLGIALPTNDIH"
     gene            3208..4631
                     /locus_tag="BT102_01385"
                     /pseudo=""
     CDS             3208..4631
                     /locus_tag="BT102_01385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005714800.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /protein_id="WP_005714800.1"
                     /codon_start=1
                     /transl_table=11
                     /product="GH1"
                     /translation="MTSLLNRVQSLPKGFVWGGATAAYQVEGATKVDGKGKTMWDDYLK
                     AQGRFSPDPASDFYHLYPEDIELAKLYGLNAIRVSIAWTRIFPDGYGEPNQAGVAYYHR
                     LFKCCLDNGITPYVSLHHFDSPKTLFDDGDWLNRKNIDYFVDYADFCFKEFPEVKNWFT
                     INELISLAFSQYIQGNFPPNHHFDVTSAIQAQHNELLAHARVVNLFKEKGYQGRIGLIH
                     VLQPVYPYPDTPANEHAAALEDAFMNRFLLDGTFKGEYTPETMALINELLKANHAKLEI
                     EPGDMDVLKQASTQNDYFGMNYYQPSFVAAYEGESTNLFNGTGEKGTSSFKFQGVGQHV
                     KNPDVPTTDWDWNIYPAGMYDMLKRVAREYPNSKTIYITENGLGYKDKYEGIGNLIEDD
                     KRIDFIDQHVAALLKARSEGVDVQGYFVWSLQDQFSWANGYNKRYGLFYVNFETQAREI
                     KKSALWFRELGKTLKAK"
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 caatttctta 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 tattattgct actgtgcttg cgcctgtctt taagggtgct
      661 gagacgtatc ctggcatgat gtttatttgg ttcttaatcc caatgttctg gttcttggga
      721 gttcatggac catcagtagt taagccggct cttgaatcag cgttgtttgg gaacaccacc
      781 gccaacttgg acttgtttaa ggctggaaac tttccatatc atgcactgac cgaaaacttt
      841 ggtaactttg ttggtgagct tggtggtacc ggtgcgacct ttattgtccc gttcctattt
      901 atgtttttca tgaaatcaaa acaattaaaa gcgattggta aagcatcgtt tatccccgtt
      961 atgttcgcgg tcaatgaacc gctgctgttt ggtgcaccga tcatcttgaa tccttacttc
     1021 ttaattccgt ttgttttggc cccagtcgtt aatgttgtga ttgggaaggc gtttattgat
     1081 ttccatatca tgagaggctt tatgtacttc atgtcgtggg cattgcctgg gccgatcggt
     1141 gcatttatcg ataccaattt ccagtggact tctttgctgc ttatggcaat tttgctaact
     1201 gtggatgcgc tgatctatat gccatttatt aaagcgtacg atgctgaatt gcttgaacaa
     1261 gaagccgctg tcgatgccgg cactgcaact gttgccgcaa gtgaaggcgc aagtgaggtc
     1321 accgctgaag cagatgcagc aacggcacaa gaattcccag aaccggaaga ggtaaagcag
     1381 gctgaaacag ctgagcaaga ggaagctaat caaaatccag ctgtaggaaa gaaactcgat
     1441 catgagttga aagtactagt gctgtgcgct ggtggtggta caagcgaaca attagccaat
     1501 gccttgactg aaggcgctaa agagtatcat gaaccaatcg ttgccagtgc aggtgcatat
     1561 gctcacatca tgatattttg ccaaactatg atctggttgt cctagcacca caagttcgaa
     1621 cctactacag tgacttaaag catgatacgg atcgtttggg gattaagctt gttgcaacta
     1681 aaggtcaaca atatatagcc ttaacgcgtg atcctgaaaa ggcattggat tttattgttg
     1741 aaaattataa ggatgtcgaa aagaaaccac aagatagttc agattcacag taaatatgtt
     1801 gacttaattt aaaatcaagc gaaaagaaag ataaggcggt gtatcgatgt tgctaaaggt
     1861 caagcaagtc tataacaata atgctgtact tgtagacgtt ggcaacggta aagaggcgat
     1921 tcttcagggg aaaggaattg gtttcagcaa gcgtaaaggt gatgacgttg atccaaaagc
     1981 gagttcggaa atactttatc taaatgatac gcaagtcaaa aatcacttta catctttact
     2041 caaagatgta ccgattgaca ttgttgttgc tacatttggt gtgatcggaa tggcaaaaaa
     2101 gaagtatcac tatccggttt tgaactatat ttatgtcacg ctcacggacc acgtctttca
     2161 gatgtataaa cgactgactg ccggcaaata tcaagctagt ccagcgcctg acatccgtga
     2221 tcgttacccg ttgccttacc agatcgcaac cgatgcgcgc cgacagctta accatgatct
     2281 tggcgttcag tttcctgaag ccgaaattaa gaatattgcc ttacatttta ttaatgcaaa
     2341 gggagtggat ggcgaactgg atccgaccgt aactctgacg gcgcgcgtca atgcaatcgt
     2401 gacacaagta tttgctaaat atgggttaaa tcgcaatttt gctaatcaaa attacttcga
     2461 tcggctaatg attcatttgc aataccttgt tgaacgttta aataccaatg agcaagacga
     2521 ggctgacctt ggtccggaaa ttggtcagga cttcaggcgc ctttatccca aatcgtttac
     2581 gatcgcaact gaaatttgta cggagctgga aaaagcctta caaattaagc tcaacgaaaa
     2641 cgaacatgtg tactttatca tccatattca gcggctcatc caagaaccgc aaacacttcc
     2701 gcctgaatat ccatagccgt gggtgggagt ttagaaagta atcttggctt agagcgattt
     2761 aggcttaaga aatcgctgct agcgtagaga attttcaaac caagggagga attttgatgg
     2821 caaccaaaga agagatttca atgaccggtt ttgcaattgt tgcttatgcc ggtgatgcga
     2881 aaaccgattt aattgaagca ttgaacgagg ctcgtaaagg caatttcgaa cacgcccgct
     2941 cacttgttaa agaagcgcgt caaagtatcg atgacgccca taatgaacag accaaacttc
     3001 ttagtaaaga ggctggtggc gagaatatgg atgttacttt catcatggtt catggccaag
     3061 atacgctaat gaccacgatg atgctgttag atacgattag tttcacgatt gatgagtatg
     3121 aacgactggc ggcaattgaa aaacaattag gcattgcatt gccaacaaac gatatccatt
     3181 aaagtatcaa acgaaaggag tatcattgtg acaagtttat tgaatcgcgt tcaatcactg
     3241 cctaaaggtt ttgtttgggg tggagcgact gctgcttatc aggtagaagg cgccaccaag
     3301 gtagacagta aaggcaaaac catgtgggat gactatctga aagctcaagg cagattttca
     3361 cctgacccag ccagtgattt ttatcatctt tatccagaag atattgaact cgccaagctc
     3421 tatgggttga atgctattcg ggtttcgatt gcctggacac ggatcttccc agatggttac
     3481 ggtgaaccta atcaagctgg ggtcgcatat tatcatcgtt tgtttaagtg ctgccttgat
     3541 aacggcatta ccccgtacgt ttcgctgcat cacttcgatt cacctaaaac gctgttcgat
     3601 gatggggatt ggctgaaccg taagaacatt gactattttg tcgattatgc tgatttctgc
     3661 tttaaagaat ttccggaagt taagaactgg ttcaccatca atgagctcat ctcgttagcc
     3721 ttttcgcaat acattcaagg caacttcccg ccaaatcatc actttgatgt taccagtgct
     3781 attcaagcgc agcacaacga actgttagcc catgcgcggg tcgtcaattt gtttaaggaa
     3841 aaaggctacc aagggcggat cggttgattc atgtgctgca gccggtttat ccttacccag
     3901 atacgccagc taatgagcat gctgctgcac ttgaagatgc cttcatgaat cggttcctgc
     3961 tggatggtac gtttaagggt gaatatacgc cggaaacgat ggcgttgatc aatgaattgc
     4021 tgaaggccaa ccatgccaag cttgaaatca aaccaggcga tatggatgtg ttgaagcaag
     4081 cgtccacgca aaatgattac tttggcatga attactatca accttctttt gttgctgcct
     4141 acgaaggtga aagcacaaat tcgtttaatg gtaccggcga gaaagggacc agttccttta
     4201 agttccaagg ggttggccag cacgtcaaaa atccggatgt gccgacgact gattgggact
     4261 ggaatattta tccggctggc atgtacgaca tgctcaaacg agtagctcgc gaatatccaa
     4321 atagcaagac gatttacatt actgaaaatg gccttggtta taaggataag tatgaaggca
     4381 ttggcaacct cattgaagat gacaaacgca tcgattttat tgatcaacat cttgctgcgt
     4441 tactaaaagc ccgcagtgag ggcgttgatg tccaaggcta ctttgtctgg tcgctgcagg
     4501 atcaattttc atgggccaat gggtataaca aacgatatgg tttattctat gtcaactttg
     4561 aaacccaagc acgcgaaatt aagaagagcg cactgtggtt tagagaatta ggaaaaacct
     4621 taaaagctta a
//
