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Alistipes putredinis DSM 17216 Scfld_02_6 genomic scaffold, whole genome shotgun sequence

GenBank: DS499576.1

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LOCUS       DS499576                3644 bp    DNA     linear   CON 16-SEP-2013
DEFINITION  Alistipes putredinis DSM 17216 Scfld_02_6 genomic scaffold, whole
            genome shotgun sequence.
ACCESSION   DS499576 ABFK02000000
VERSION     DS499576.1
DBLINK      BioProject: PRJNA19655
            BioSample: SAMN00000002
KEYWORDS    WGS.
SOURCE      Alistipes putredinis DSM 17216
  ORGANISM  Alistipes putredinis DSM 17216
            Bacteria; Pseudomonadati; Bacteroidota; Bacteroidia; Bacteroidales;
            Rikenellaceae; Alistipes.
REFERENCE   1  (bases 1 to 3644)
  AUTHORS   Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M.,
            Liep,D. and Gordon,J.
  TITLE     Draft genome sequence of Alistipes putredinis (DSM 17216)
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3644)
  AUTHORS   Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Pepin,K.H.,
            Johnson,M., Thiruvilangam,P., Bhonagiri,V., Nash,W.E., Mardis,E.R.
            and Wilson,R.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2007) Genome Sequencing Center, Washington
            University School of Medicine, 4444 Forest Park, St. Louis, MO
            63108, USA
COMMENT     Alistipes putredinis (GenBank Accession Number for 16S rDNAgene:
            L16497) is a member of the Bacteroidetes division of the domain
            bacteria and has been isolated from human feces. It has been found
            in 16S rDNA sequence-based enumerations of the colonic microbiota
            of adult humans (Eckburg et. al.(2005), Ley et. al. (2006)). The
            sequenced strain was obtained from Deutsche Sammlung von
            Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 17216).
            
            We have collected 11.6X coverage in plasmid end reads and454 reads.
            We have performed one round of automated sequence
            improvement(pre-finishing), along with manual improvement that
            includes breaking apart any mis-assembly, and making manual joins
            where possible. Manual edits also are made where the consensus
            appears to be incorrect. All low quality data on the ends of
            contigs is removed. Contigs are ordered and oriented where
            possible.
            
            Sequencing/Assembly: The genomic DNA was purified from liquid
            culture derived from a single bacterial colony. A hybrid sequencing
            strategy that utilized reads from both 454 GS-20 and ABI 3730xl
            sequencers was devised and implemented to generate the draft genome
            sequences.  454 reads were assembled using Newbler (454 Life
            Sciences) into 454 de novo contigs. These de novo contigs were
            converted in silico to 800 base paired reads ('superreads') with
            400 base overlaps with neighboring superreads.  Finally, PCAP
            (Huang, et al, Genome Research, 13:2164, (2003)) was used to
            assemble the super-reads and the conventional 3730xl capillary
            reads.
            
            This sequenced strain is part of a comprehensive, sequence-based
            survey of members of the normal human gut microbiota.  A joint
            effort of the WU-GSC and the Center for Genome Sciences at
            Washington University School of Medicine, the purpose of this
            survey is to provide the general scientific community with a broad
            view of the gene content of 100 representatives of the major
            divisions represented in the intestine's microbial community. This
            information should provide a frame of reference for analyzing
            metagenomic studies of the human gut microbiome. Further details of
            this effort are described in a white paper entitled 'Extending Our
            View of Self: the Human Gut Microbiome Initiative (HGMI)'
            (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMIS
            eq.pdf). These studies are supported by National Human Genome
            Research Institute.
            
            For answers to your questions regarding this assembly or project,
            or any other GSC genome project, please visit our Genome Groups web
            page (http://genome.wustl.edu/genome_group_index.cgi) and email the
            designated contact person.
FEATURES             Location/Qualifiers
     source          1..3644
                     /organism="Alistipes putredinis DSM 17216"
                     /mol_type="genomic DNA"
                     /strain="DSM 17216"
                     /type_material="type strain of Bacteroides putredinis"
                     /db_xref="taxon:445970"
     gene            complement(<1..132)
                     /locus_tag="ALIPUT_00021"
     CDS             complement(<1..132)
                     /locus_tag="ALIPUT_00021"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="EDS04820.1"
                     /translation="MKKLHHIVLVLALAATLFTGCNKDEGVTPRPPVPETADQTIMFY
                     "
     gene            complement(310..1047)
                     /locus_tag="ALIPUT_00022"
     CDS             complement(310..1047)
                     /locus_tag="ALIPUT_00022"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="EDS04821.1"
                     /translation="MRKLLVLLLFLPLMATAKIPVEEDIIRQTLDSESPYYYPNLMLR
                     YQSGDDSMTEEDYHYLYYGYAYQDAYKPLNANSDMDKAILIAQTVDFENPTHESLEKL
                     IAAVNDALVQDPFSPKLLNLLAFAYGALGDSKNEQINYNRMNSILATIEDSGNGLKEG
                     SAWHILMFGHALDLLAAHDRHYGKARVVSRSVEYVPLLEPVRTEEGRIKGYYFDYSRI
                     YRNKPDDYVFKRPRTWQFNNLRPREYK"
     gene            complement(1127..1579)
                     /locus_tag="ALIPUT_00023"
     CDS             complement(1127..1579)
                     /locus_tag="ALIPUT_00023"
                     /inference="protein motif:Gene3D:IPR013785"
                     /inference="protein motif:HMMPanther:IPR002220"
                     /inference="protein motif:HMMPfam:IPR002220"
                     /inference="similar to AA sequence:REFSEQ:YP_001300553.1"
                     /note="KEGG: bfs:BF2486 5.5e-28 dapA2; putative
                     dihydrodipicolinate synthase K01714;
                     COG: COG0329 Dihydrodipicolinate
                     synthase/N-acetylneuraminate lyase"
                     /codon_start=1
                     /transl_table=11
                     /product="dihydrodipicolinate synthetase family"
                     /protein_id="EDS04822.1"
                     /db_xref="InterPro:IPR002220"
                     /db_xref="InterPro:IPR013785"
                     /translation="MTAATTIRIAGDFPNVIGIKEASGKIDQIQEILDWRSRDFLVLS
                     GDDALTLDLMSRGADGVISVAVNAFPRKMMTCIDLAKKGDFEGAHKAYECLEEAVTAL
                     FAEGNPTGVKCAMSVLGLIGNTLRLPLVPGTPQLEARFKELIAKYDLN"
     gene            complement(1702..1899)
                     /locus_tag="ALIPUT_00024"
     CDS             complement(1702..1899)
                     /locus_tag="ALIPUT_00024"
                     /note="KEGG: bfs:BF3862 0.0034 dapA1; putative
                     dihydrodipicolinate synthase K01714;
                     Psort location: Cytoplasmic, score: 8.96"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="EDS04823.1"
                     /translation="MWISSCNSARRQNPDPLPARTGRCRHVHQNHIAGRVPLVIGVGG
                     NSTSEVLDQLREFDRGGRMRS"
     gene            complement(2368..3339)
                     /locus_tag="ALIPUT_00019"
     CDS             complement(2368..3339)
                     /locus_tag="ALIPUT_00019"
                     /inference="protein motif:HMMPfam:IPR001357"
                     /inference="protein motif:HMMSmart:IPR001357"
                     /inference="protein motif:superfamily:IPR010994"
                     /inference="similar to AA sequence:INSD:ABR40932.1"
                     /note="KEGG: bfs:BF2485 1.1e-54 ligA, dnaL, lig, lop,
                     pdeC; putative DNA ligase K01972;
                     COG: COG0272 NAD-dependent DNA ligase (contains BRCT
                     domain type II);
                     Psort location: Cytoplasmic, score: 8.96"
                     /codon_start=1
                     /transl_table=11
                     /product="BRCA1 C-terminal domain protein"
                     /protein_id="EDS04824.1"
                     /db_xref="InterPro:IPR001357"
                     /db_xref="InterPro:IPR010994"
                     /translation="MDIEGLGEETVELLFENGLLHDIADLYDLRAEQLACLPRLGEKS
                     AENIIRSIRGSVEVPFQRVLFALGIRFVGETTAKYLAAHFRTLDAVMHATREELIEAD
                     EVGGKIADAIIDYFADAENLRIIERLRKAGLQTEAAHKALESESLAGKNFVITGRFSG
                     HSRDELKELIEAHGGKNLAGVSGNVEFLVAGKKIGPGKIQKATQLGVRLIPEEELLAM
                     NASGGTLPVTKKSFRREHLCGPPPRLRETTDKNDGGGHGKRGRCFLGGNGTPRGRENT
                     QYYFPGACPGHRNNDVEIRIIRTNPFSLLRSPGFWAGSFPLLPKRKF"
     gene            3358..>3644
                     /locus_tag="ALIPUT_00020"
     CDS             3358..>3644
                     /locus_tag="ALIPUT_00020"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="EDS04825.1"
                     /translation="MDDAAQYLRPAVALIGTVVLAFALVFHQRSAAFRTAGDVLEGTA
                     VRRTGRKIDARDLGDDLAAFFDIYHIAYANVQQGDLFGVVQRGPNPPQCELA"
CONTIG      join(ABFK02000014.1:1..2106,gap(unk100),ABFK02000013.1:1..1438)
//
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