GenomeNet

Database: RefSeq
Entry: NC_015699
LinkDB: NC_015699
Original site: NC_015699 
LOCUS       NC_015699               7047 bp    DNA     circular CON 30-JUL-2015
DEFINITION  Lactobacillus reuteri SD2112 plasmid pLR580, complete sequence.
ACCESSION   NC_015699 NZ_ACGW02000000 NZ_ACGW02000001 NZ_ACGW02000002
            NZ_ACGW02000003 NZ_ACGW02000004 NZ_ACGW02000005 NZ_ACGW02000006
            NZ_ACGW02000007 NZ_ACGW02000008 NZ_ACGW02000009 NZ_ACGW02000010
            NZ_ACGW02000011 NZ_ACGW02000012 NZ_ACGW02000013 NZ_ACGW02000014
VERSION     NC_015699.1  GI:338202351
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN00001494
            Assembly: GCF_000159455.2
KEYWORDS    RefSeq.
SOURCE      Lactobacillus reuteri SD2112
  ORGANISM  Lactobacillus reuteri SD2112
            Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
            Lactobacillus.
REFERENCE   1  (bases 1 to 7047)
  AUTHORS   Muzny,D., Qin,X., Buhay,C., Dugan-Rocha,S., Ding,Y., Chen,G.,
            Hawes,A., Holder,M., Jhangiani,S., Johnson,A., Khan,Z., Li,Z.,
            Liu,W., Liu,X., Perez,L., Shen,H., Wang,Q., Watt,J., Xi,L., Xin,Y.,
            Zhou,J., Deng,J., Jiang,H., Liu,Y., Qu,J., Song,X.-Z., Zhang,L.,
            Villasana,D., Johnson,A., Liu,J., Liyanage,D., Lorensuhewa,L.,
            Robinson,T., Song,A., Song,B.-B., Dinh,H., Thornton,R., Coyle,M.,
            Francisco,L., Jackson,L., Javaid,M., Korchina,V., Kovar,C.,
            Mata,R., Mathew,T., Ngo,R., Nguyen,L., Nguyen,N., Okwuonu,G.,
            Ongeri,F., Pham,C., Simmons,D., Wilczek-Boney,K., Hale,W.,
            Jakkamsetti,A., Pham,P., Ruth,R., San Lucas,F., Warren,J.,
            Zhang,J., Zhao,Z., Zhou,C., Zhu,D., Lee,S., Bess,C.,
            Blankenburg,K., Forbes,L., Fu,Q., Gubbala,S., Hirani,K.,
            Jayaseelan,J.C., Lara,F., Munidasa,M., Palculict,T., Patil,S.,
            Pu,L.-L., Saada,N., Tang,L., Weissenberger,G., Zhu,Y., Hemphill,L.,
            Shang,Y., Youmans,B., Ayvaz,T., Ross,M., Santibanez,J., Aqrawi,P.,
            Gross,S., Joshi,V., Fowler,G., Nazareth,L., Reid,J., Worley,K.,
            Petrosino,J., Highlander,S. and Gibbs,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2011) Human Genome Sequencing Center, Baylor
            College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
COMMENT     REFSEQ INFORMATION: The reference sequence was derived from
            CP002848.
            Lactobacillus reuteri SD2112
            
             Strain source, body site: Gastrointestinal tract
            
             Inquiries should be directed to microbe@hgsc.bcm.tmc.edu
            
             This is a reference genome for the Human Microbiome Project. This
            project is co-owned with the Human Microbiome Project DACC.  Source
            DNA provided by Versalovic, J. (Department of Pathology, Texas
            Children's Hospital, 1102 Bates Avenue, Suite 830, Feigin Center,
            Houston, TX, 77030, USA).  Funded by by 'Genomes and Genetics at
            BCM-HGSC' (U54 HG003273).
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Assembly-Data-START##
            Finishing Goal           :: Finished
            Current Finishing Status :: Finished
            Assembly Method          :: Newbler Assembler v. 2.3.10192009
            Genome Coverage          :: 63x
            Sequencing Technology    :: 454
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider                    :: NCBI
            Annotation Date                        :: 07/30/2015 18:55:05
            Annotation Pipeline                    :: NCBI Prokaryotic Genome
                                                      Annotation Pipeline
            Annotation Method                      :: Best-placed reference
                                                      protein set; GeneMarkS+
            Annotation Software revision           :: 3.0
            Features Annotated                     :: Gene; CDS; rRNA; tRNA;
                                                      ncRNA; repeat_region
            Genes                                  :: 2,314
            CDS                                       2,116
            Pseudo Genes                           :: 82
            rRNAs                                  :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                         :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                                  :: 69
            ncRNA                                  :: 29
            Frameshifted Genes                     :: 34
            Frameshifted Genes On Monomer Runs     :: 3
            Frameshifted Genes Not On Monomer Runs :: 5
            ##Genome-Annotation-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..7047
                     /organism="Lactobacillus reuteri SD2112"
                     /mol_type="genomic DNA"
                     /strain="SD2112"
                     /isolation_source="biological product [ENVO:02000043]"
                     /host="Homo sapiens"
                     /db_xref="taxon:491077"
                     /plasmid="pLR580"
     gene            complement(join(6394..7047,1..1485))
                     /locus_tag="HMPREF0538_RS11585"
     CDS             complement(join(6394..7047,1..1485))
                     /locus_tag="HMPREF0538_RS11585"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_003672547.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_003672547.1"
                     /db_xref="GI:489768625"
                     /translation="MAIKIKDSSKTLSGKFDTYIKSQYKFLSLVHAGAINGLLTVTKP
                     KDNKHKHNFKHQPILSDNGDLGYEQYYHLDMTDNVVIPHVTMVYSNGANTAGRVVYID
                     NTRIAHSPLRELNEASKRTQTMVKVLDTAKQLQQIRSGSSEFCSYMTTLTIPNCNKDE
                     LDQVVGSMSTRITAVIKALQDGYRNGNGLRLVDHNGRPVQILGAIVKIEITINQVKLK
                     TCDSQGIFHPHIHIVLITANELALGPSRRILFHYWSNKNSDMILSRKAFNFKKAYSKN
                     QMDSDDSTSIVAEATKYATKPTMYKLLPTIKDSNNLTSDDQFKLEIFCEVFKTIKGRQ
                     LSRSYGLIRDATGFVNFLKNGIMVKYRGNNPMHGKHERISIFDAFMFGNYNDNKQIHV
                     PDIMTTRNELIPGGNFNQVDLSDDELLYANKGLLSGATWELPDNIKWPSNNQKADEYK
                     ELLTRFGFVQPGLGNIIDQLQSWIQTIDQRKDKVLHTVLDASERSFQYNDLLHKGEDV
                     RRLVRILEDVCDQYGDDTTTLTTHDYSQIYRDVDLMQVMDAHHATLHYDSYGKPDDVT
                     FDEPDVERRLVASYKKHDDVRFMSATAFLPREILIEYGVWLKHTPSEFIDNLASYTSH
                     APELEIDTVSKMDAKTTQKWINKAFNVSSSNGPQIDFHTMFTSAKMSQVQADNNDDLD
                     HLFDDGVGDDDDDDNTEINSLSDVFPDLKW"
     gene            complement(1978..2475)
                     /locus_tag="HMPREF0538_RS11590"
                     /old_locus_tag="HMPREF0538_22305"
     CDS             complement(1978..2475)
                     /locus_tag="HMPREF0538_RS11590"
                     /old_locus_tag="HMPREF0538_22305"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_003672548.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_003672548.1"
                     /db_xref="GI:489768626"
                     /translation="MDRHVWQRLATVVLAALVIFSINTFSPVGNGDGLGITTIQAKKK
                     THQLPNLLDQQIAILVGLDINPNWVREQSAADSLIYGIVKPDDTVPAGINEDYSYLVT
                     SNRDKEISLFFKADKKKVTIKYANHGEKLHTKTVPLSRLVEQSYRTKKQRQQVNKYAS
                     ALRTE"
     gene            complement(2965..3522)
                     /locus_tag="HMPREF0538_RS11595"
                     /old_locus_tag="HMPREF0538_22306"
     CDS             complement(2965..3522)
                     /locus_tag="HMPREF0538_RS11595"
                     /old_locus_tag="HMPREF0538_22306"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_003672549.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_003672549.1"
                     /db_xref="GI:489768627"
                     /translation="MIFDGPWDDDERYILDDRQLYFLKQAGERLSSQDFQDLKQENDD
                     ELGFYSCTVDGELDRKKLPSSFLEVKVRVGRKLRSQIKQMVDDPDKLPEFGFRDYRGM
                     TVTDCEYLSLLELPDEWLSNYLRYFMNYSGIHSDDVYVAASGRFKLVEIDNWKNVVPD
                     YSDFSTVDLLQCDMNFLKAYIASIE"
     gene            complement(3560..4057)
                     /locus_tag="HMPREF0538_RS11600"
                     /old_locus_tag="HMPREF0538_22307"
     CDS             complement(3560..4057)
                     /locus_tag="HMPREF0538_RS11600"
                     /old_locus_tag="HMPREF0538_22307"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_003672551.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_003672551.1"
                     /db_xref="GI:489768629"
                     /translation="MNTKNQVKTKTKTYTTSELASLCGVTVGSISVLIKKQNLKPVKT
                     GQNNAKYYDAGVLKQLRLHYAKSKPKRDKTNNTQDLRTQLAVAQSENQLLRDQLESAK
                     STIEILRNELKIKNSQIDKLQDLTNQAQQLDLATHTQHQELLEQKSQPTDEPTKHKHG
                     IFNWF"
     gene            complement(4075..5568)
                     /locus_tag="HMPREF0538_RS11605"
                     /old_locus_tag="HMPREF0538_22308"
     CDS             complement(4075..5568)
                     /locus_tag="HMPREF0538_RS11605"
                     /old_locus_tag="HMPREF0538_22308"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_013924050.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_013924050.1"
                     /db_xref="GI:503689974"
                     /translation="MSSITFENSFQGSFRDMGESHISIHSGQHDNMVDGEDPIIELRG
                     NSVSDSSWALMIAKATSQGVVSPKDWPEYNRKIPDKKRRKKDYNDYLLTLCSKPIKRL
                     KATQTAKNTPKAQRTKISQELASVDRDHVLNDGSLWYVAKVDDRPDNVGKKEWREFEV
                     EALTRFDKDPTYRMLNPGTYRSEIHLDERGEIHKQDLAVWFRPDSRGRVQYSKTSTIQ
                     DVLLKLYGGNKDELDRRVSLVSEITNNIDKTPGQERADTKLWRSVKSNQQPTRMLHAG
                     KRYNSAMITLWRYENVRILRDTALQVAKERGIDYQVSDRYETDGVHRSRDIYMQHQQA
                     KDSLHGEQLKKKRAQYATGKLIDAINDIYRDTLKRDPGASESPLEQTNKIINHLNEIK
                     EESKRIQRENDRQQQQLDQLKRQNELMKRQQFRWFELRLLIVNIIEKLWHLMFDRDLQ
                     HDFTNDHQKWRDSMTNQVNKEMYNQLDQDQQKQLNAPNQSNGHNLER"
     gene            complement(5877..6131)
                     /locus_tag="HMPREF0538_RS11610"
                     /old_locus_tag="HMPREF0538_22309"
     CDS             complement(5877..6131)
                     /locus_tag="HMPREF0538_RS11610"
                     /old_locus_tag="HMPREF0538_22309"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_003672544.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_003672544.1"
                     /db_xref="GI:489768622"
                     /translation="MKIFKKKCVLLEAAGRPLGERKLCKFYLHNIIAWYNRYVKSETF
                     HENSLSFSIDDTLKCADFTGFFNFDGFTIEPRFDFILSLD"
CONTIG      join(CP002848.1:1..7047)
//
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