LOCUS       MSTC01000081            4566 bp    DNA     linear   BCT 01-FEB-2017
DEFINITION  Lactobacillus rhamnosus strain AMC010 contig_58, whole genome
            shotgun sequence.
ACCESSION   MSTC01000081
VERSION     MSTC01000081.1
DBLINK      BioProject: PRJNA357881
            BioSample: SAMN06161582
KEYWORDS    WGS.
SOURCE      Lactobacillus rhamnosus
  ORGANISM  Lactobacillus rhamnosus
            Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
            Lactobacillus.
REFERENCE   1  (bases 1 to 4566)
  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  JOURNAL   Unpublished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 4566)
  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..4566
                     /organism="Lactobacillus rhamnosus"
                     /mol_type="genomic DNA"
                     /submitter_seqid="contig_58"
                     /strain="AMC010"
                     /isolation_source="infant stools"
                     /host="Homo sapiens"
                     /db_xref="taxon:47715"
                     /country="USA"
                     /collection_date="2011"
     gene            1..879
                     /locus_tag="BVG98_13950"
     CDS             1..879
                     /locus_tag="BVG98_13950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003660216.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcription antiterminator lact"
                     /protein_id="ONF98579.1"
                     /translation="MPKIAQIFNNNVALVDLDNRGQAVVRGRGIAFQKRRGAVIPTKQI
                     EKIFYLANETSRQNLYFLLKNIPIDVVTTTYEIIDVAQKQYRLKVLDYIYITLSDHIYE
                     AYKRYQAGTYQETMVPDFHIQYPAEYAVAKQALQIIATNLGVQFPQSEIKNLALHFINA
                     SGEDDGEQVFGKSNEASLSQLVQEVLKRHHITRSHSNGNYYDRFMIHLQYLIDRLQRVD
                     TYAVTIVPEVATELKQNYPQSYKIASEIFDEIKDQLYRSMSEDERLYFIIHIQRLINEA
                     PAQNHSQNDSL"
     gene            1000..2731
                     /locus_tag="BVG98_13955"
                     /pseudo=""
     CDS             1000..2731
                     /locus_tag="BVG98_13955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005691812.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /protein_id="WP_005691812.1"
                     /codon_start=1
                     /transl_table=11
                     /product="PTS lactose transporter subunit IIB"
     gene            2758..4182
                     /locus_tag="BVG98_13960"
     CDS             2758..4182
                     /locus_tag="BVG98_13960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003589794.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GH1"
                     /protein_id="ONF98580.1"
                     /translation="MSKQLPQDFVMGGATAAYQVEGATKEDGKGRVLWDDFLDKQGRFK
                     PDPAADFYHRYDEDLALAEKYGHQVIRVSIAWSRIFPDGAGEVEPRGVAFYHKLFADCA
                     AHHIEPFVTLHHFDTPERLHEAGDWLSQEMLDDFVAYAKFCFEEFSEVKYWITINEPTS
                     MAVQQYTSGTFPPAESGRFDKTFQAEHNQMVAHARIVNLYKSMQLGGQIGIVHALQTVY
                     PYSDSAVDHHAAELQDALENRLYLDGTLAGEYHQETLALVKEILDANHQPMFQSTPQEM
                     KAIDEAAHQLDFVGVNNYFSKWLRAYHGKSETIHNGDGTKGSSVARLQGVGEEKLPDGI
                     ETTDWDWSIYPRGMYDILMRIHNDYPLVPVTYVTENGIGLKESLPENATPDTVIEDPKR
                     IDYVKKYLSAMADAIHDGANVKGYFIWSLQDQFSWTNGYSKRYGLFFVDFPTQNRYIKQ
                     SAEWFKSVSETHIIPD"
     gene            4231..4566
                     /locus_tag="BVG98_13965"
     CDS             4231..4566
                     /locus_tag="BVG98_13965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003589792.1"
                     /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="ONF98581.1"
                     /translation="MATKEEISMVGFALVAYAGDARTAAVHALDAAEAGDFDKANELVE
                     KAQQDINEAHNQQTQLLSQEAGGAEMDVTFIMVHGQDTLMTTMLLIDETRYMIRMFKRI
                     KELENKQ"
ORIGIN
        1 ttgccaaaaa tagctcagat ttttaacaac aacgtggcct tggttgatct agacaaccgc
       61 ggccaagccg ttgtaagggg acgtggcatc gcttttcaga agaggcgagg agctgttatt
      121 ccgacaaagc agatagagaa gatcttttat ctagcgaacg agacttcccg acaaaatttg
      181 tactttctct taaaaaatat tccgattgac gtggtgacga ctacctatga aattattgat
      241 gttgcccaga aacaatatcg actgaaagtg cttgattata tctacattac cttgagtgat
      301 catatttacg aggcatataa acgctatcag gcagggactt atcaagaaac aatggtacca
      361 gattttcata ttcaatatcc ggccgaatat gcggtggcta aacaggcact gcaaatcatt
      421 gccacgaacc ttggcgttca gtttccacag tcggaaataa aaaatctggc gttgcacttt
      481 atcaacgctt ccggtgaaga cgatggcgag caggtttttg gtaaaagcaa tgaagcctca
      541 cttagtcaac ttgtacaaga agtgttgaag cgtcatcaca ttactcgctc tcattcaaat
      601 ggcaactact atgaccggtt tatgattcat ctccagtatc tcatcgaccg actgcagcgt
      661 gttgatacat atgccgttac cattgtccct gaggttgcca ctgaacttaa gcaaaactat
      721 ccgcagtctt acaagattgc ctcagaaatt ttcgatgaaa ttaaggatca actctatcgc
      781 agtatgagtg aggacgaacg actttacttc atcatccaca ttcagcgatt gataaacgaa
      841 gcaccagccc agaatcattc acaaaacgat tcattataac gcgctcgcag tcgtagaagc
      901 ctacacataa gggctttgaa gcaatctacc aaagattggg ccagtttgct tcaagcacgc
      961 ttatgctttg gcttccaagc gctcaggagg aaaagactca tgaataaggt ttttgataaa
     1021 ttaaaaccgg tttttgaagc catcgctgct aacaaatata tttccgcgat tcgtgatggc
     1081 tttatcgcat gtatgccgat catcatcttc tcaagtatct ttatgatggt tgcttatgtt
     1141 ccgaacgctt gggggtttta ctggccagac aacgtaacga atacgttgat ggttgcttat
     1201 aactattcca tgggcttgct ggcactgttt gtggcgggaa cgactgctaa aaacttgact
     1261 gacagcaaga accttgaatt accgaaaaca aatcaaatta atccagtggc cgtcattgtg
     1321 gcgtctgaaa tttcttttgt cattttgtcg atcttgccgc ttaaaaccgg tgttgacctg
     1381 acttacatgg ggactcaggg attgatctgc gcttatatcg ttgggttgat cgtgccaaat
     1441 atttactacg tctgtattaa gaacaatgtc acgattaaat taccagcgca ggtaccaggt
     1501 aatatcgccc agtcatttaa agaccttatc ccgatgggcc tttctgtgac agccttctgg
     1561 cttttcggtg ttggcttcaa agcggcaacg ggtactgtat tgccacgctg gatcattcaa
     1621 gtactttcgc cgcttttcca agccagcgat tcttatctag gcttagcctg attgctggcg
     1681 cgatggcttt cttctggttc tgtggtgtcc aaggcccatc aattgttcag ccggctgttg
     1741 tcccgattat gattgcgaat acagcagcta acttgcagca atatcaggca gggcaacatg
     1801 tctcgcacgt tttggccatg aacacgatgg actacgtcat gaattttggt ggaaccggag
     1861 caacattggt ggtacctttc atcatgctgt ttgcggcccg atcagcgcaa ttaaaagccg
     1921 ttggtaaggc ttcctttgtg ccatgcactt tcggggtcaa tgaacctgtt ttgtttggaa
     1981 tgccgattat catgaatccc attttcttca ttccgttctt agcaaccccg atcgtgaacg
     2041 tttgcttatt caaattcttt gtgagtgtac ttggcatgaa cagtatgatg tacaccatgc
     2101 catggacagt tccgggaccg attgggattt tgatttcgac tgggtttgcc ccgttggctt
     2161 tcgcctttgt tctactgacg ttggttctgg acgttgcgat atacttccca ttcattcgcg
     2221 tttatgacag cacactctta gctgaagaaa aagctaggga agaggtcatt gaagacgacg
     2281 gcattgctgt tcaggcgagt gacacagtgt caccttctat cccgactggt ttgactgttg
     2341 cgactgccac agacgacgat gcgacccatg tgttgcctga aacagcccca tctgcccacg
     2401 gcgaagctat ttcaaacaaa atgaagttaa tgttttagtg ttgtgtgctg gtggtggaac
     2461 aagcggtatt cttgccaacg cgctaaacaa actgtctaag gaacgcggtt taaagctctc
     2521 ggccgccgcc cgcgcttatg gacaggatat ggatttgatc aaagatatga acatggtcat
     2581 ccttgcgccg caaatggaaa gcatgaaagg taatttaaaa aagatcaccg ataagtatgg
     2641 cgtcaagctg gtcacaacaa ctggtcggca atacattgaa ttaaccaaca atggtgacaa
     2701 ggcacttgat tttgttgaat ccaatctttg agacacttaa caggaggtta ttaagcaatg
     2761 agtaaacagc tacctcaaga ttttgtaatg ggcggggcaa ccgccgccta tcaagtcgaa
     2821 ggagccacca aggaagacgg taaaggtcgc gtgctttggg acgattttct ggataaacag
     2881 gggcggttca agcccgaccc ggcagcggat ttttatcatc gttatgatga agatttggca
     2941 ttagcggaaa aatacggcca tcaagtgatt cgggtgtcaa ttgcctggtc gcgaattttt
     3001 ccggatggtg ccggggaagt tgagccacgc ggggttgctt tttaccacaa gctcttcgcg
     3061 gattgtgccg cccatcatat cgaaccgttt gttacgctac atcattttga tacgcccgaa
     3121 cgcttgcacg aagccggtga ttggttgagt caagagatgt tggacgactt tgtggcttat
     3181 gcgaagtttt gctttgaaga attttccgaa gtgaagtatt ggatcaccat taatgaaccg
     3241 acctcaatgg ccgttcaaca atatacaagc gggacattcc cgcctgccga gtctggacgt
     3301 tttgataaga cgttccaagc tgaacacaat caaatggtgg cgcatgcccg tatcgttaat
     3361 ctatataagt caatgcaatt aggtggccaa attggaattg ttcatgcgtt gcaaactgtt
     3421 tatccctaca gtgatagcgc tgtggatcac catgccgccg agttgcagga cgctttggaa
     3481 aatcgattgt atctggatgg cacattagct ggcgaatatc accaagaaac tttggcgctc
     3541 gtgaaggaaa ttctggatgc caatcatcaa ccgatgtttc aatcgacacc gcaggaaatg
     3601 aaggctattg atgaagcggc ccatcagtta gactttgttg gggtcaataa ttatttcagc
     3661 aagtggttgc gtgcctatca tggcaaatca gagaccattc ataatggcga cggcaccaaa
     3721 ggctcttcgg tcgcgcggct gcaaggcgtc ggcgaggaaa aactcccaga tggcattgag
     3781 acgacagatt gggattggtc gatttatcca cgaggaatgt atgacatact gatgcggatt
     3841 cataatgact atccgttggt gccagtgacc tacgtgacag aaaatggtat tggtcttaaa
     3901 gaaagcttgc cagaaaatgc gacccctgac accgtgattg aagatccaaa acggattgat
     3961 tatgtaaaga aatatctgtc cgcaatggct gatgctatcc atgatggcgc aaatgtcaaa
     4021 ggttacttca tctggtcact tcaagatcag ttttcttgga caaacggtta cagtaaacga
     4081 tatggtctgt tcttcgttga ttttccaaca caaaatcgtt atatcaaaca aagtgccgag
     4141 tggtttaagt ctgtgagtga gacccacatc attccggatt aaaaagtttt tggctattta
     4201 gacagcaagg attgaatcgg agggaaaatg atggctacta aagaagaaat ttcaatggtt
     4261 ggttttgcac ttgtggcgta tgcaggcgat gctcgaacgg ctgctgtgca tgcacttgat
     4321 gccgctgaag caggcgattt cgataaggca aacgaattgg ttgagaaggc ccaacaggat
     4381 atcaatgaag cccacaacca acagacccag cttctaagtc aagaagcggg cggtgctgaa
     4441 atggatgtca cctttatcat ggttcatggt caagatacgt tgatgacaac catgttgctc
     4501 attgatgaaa cacgctacat gattcgcatg tttaagcgga tcaaagaact tgagaacaag
     4561 cagtaa
//
